9F5Y | pdb_00009f5y

Structure of the Chlamydomonas reinhardtii respiratory complex I from respiratory supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

In-cell architecture of the mitochondrial respiratory chain

Waltz, F.Righetto, R.Lamm, L.Salinas-Giege, T.Kelley, R.Zhang, X.Obr, M.Khavnekar, S.Kotecha, A.Engel, B.D.

(2025) Science 


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 24 kD subunit282Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial484Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 78 kDa subunit733Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein282Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 49 kD subunit467Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit 10164Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase subunit 8231Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
B14.5a118Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 18 kDa subunit165Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinJ,
RA [auth r]
128Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase B14 subunit138Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial187Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 13 kD-like subunit154Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12156Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase B8 subunit101Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Putative NADH:ubiquinone oxidoreductase 39 kDa subunit397Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1292Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2387Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3279Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4443Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 4L227Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5546Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6162Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ASHI149Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
P964Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
KFYI124Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
AGGGAA [auth a]129Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
ESSSBA [auth b]172Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
B9CA [auth c]67Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 10 kDa subunitDA [auth d]86Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 23 kDa subunitEA [auth e]219Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 7.5 kDa subunitFA [auth f]65Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial putative NADH:ubiquinone oxidoreductase 6.5 kDa subunitGA [auth g]55Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 13 kDa subunitHA [auth h]142Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 15 kDa subunit-likeIA [auth i]81Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7JA [auth j]86Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9KA [auth k]117Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 20,9 kD-like subunitLA [auth l]121Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13MA [auth m]142Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Putative NADH:ubiquinone oxidoreductase 12.5 kDa subunitNA [auth n]106Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Putative NADH:ubiquinone oxidoreductase 17.8 kDa subunitOA [auth o]155Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 16 kDa subunitPA [auth p]130Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
UniProt
Find proteins for Q6QAY0 (Chlamydomonas reinhardtii)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 19 kDa subunitQA [auth q]197Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
UniProt
Find proteins for Q6QAY1 (Chlamydomonas reinhardtii)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 32 kDa subunitSA [auth s]312Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
UniProt
Find proteins for Q6S7R7 (Chlamydomonas reinhardtii)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
CAG2 - CA-likeTA [auth t]279Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8JFK6 (Chlamydomonas reinhardtii)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
CAG1UA [auth u]229Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8JHY4 (Chlamydomonas reinhardtii)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
P10VA [auth v]45Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial NADH:ubiquinone oxidoreductase 9 kDa subunitWA [auth w]109Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
NUOP8XA [auth x]157Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8IS53 (Chlamydomonas reinhardtii)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
NUOP7YA [auth y]118Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
AD [auth y]
DC [auth V]
HC [auth W]
PC [auth h]
RB [auth R]
AD [auth y],
DC [auth V],
HC [auth W],
PC [auth h],
RB [auth R],
VC [auth u],
WC [auth u],
YC [auth x]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
COO
Query on COO

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SC [auth s]CROTONYL COENZYME A
C25 H40 N7 O17 P3 S
KFWWCMJSYSSPSK-XBTRWLRFSA-N
PC7
Query on PC7

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MB [auth Q],
PB [auth R],
UC [auth u],
XB [auth T]
(7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
C42 H85 N O8 P
PZNPLUBHRSSFHT-FAIXQHPJSA-O
PGT
Query on PGT

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IC [auth b],
QC [auth l],
WB [auth T],
ZB [auth T]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
NDP
Query on NDP

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KB [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PTY
Query on PTY

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AC [auth T]
EC [auth V]
FC [auth V]
GC [auth V]
IB [auth G]
AC [auth T],
EC [auth V],
FC [auth V],
GC [auth V],
IB [auth G],
KC [auth e],
LC [auth e],
OB [auth R],
OC [auth h],
QB [auth R],
SB [auth R],
UB [auth S],
VB [auth T],
YB [auth T],
ZC [auth x]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
3PH
Query on 3PH

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BC [auth V]
CC [auth V]
JC [auth c]
MC [auth g]
NB [auth R]
BC [auth V],
CC [auth V],
JC [auth c],
MC [auth g],
NB [auth R],
NC [auth h],
TB [auth S],
XC [auth w]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
8Q1
Query on 8Q1

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JB [auth J],
RC [auth r]
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
UQ5
Query on UQ5

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LB [auth Q]2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE
C34 H50 O4
NYFAQDMDAFCWPU-UVCHAVPFSA-N
FMN
Query on FMN

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AB [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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BB [auth B]
DB [auth C]
EB [auth C]
FB [auth F]
GB [auth G]
BB [auth B],
DB [auth C],
EB [auth C],
FB [auth F],
GB [auth G],
HB [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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CB [auth C],
ZA [auth A]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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TC [auth s]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Alexander von Humboldt FoundationGermany--
Swiss National Science FoundationSwitzerland210561

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release