8UCN | pdb_00008ucn

Komagataella pastoris Cytochrome c oxidase in complex with human VMAT2 and Histamine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Molecular basis of vesicular monoamine transport and neurological drug interactions.

Ye, J.Chen, H.Ammerman, A.Wang, Y.Wang, K.Xu, J.Liu, B.Li, W.

(2025) Cell Rep 44: 116490-116490

  • DOI: https://doi.org/10.1016/j.celrep.2025.116490
  • Primary Citation Related Structures: 
    8UCN

  • PubMed Abstract: 

    Vesicular monoamine transporter 2 (VMAT2) stores monoamine neurotransmitters in synaptic vesicles to regulate their release. VMAT2 is a primary target in neurological disorder treatment and contributes to amphetamine-induced psychostimulation. Here, we report cryo-electron microscopy structures of human VMAT2 capturing a cytoplasmic-open state with reserpine and lumenal-facing states with serotonin and histamine in open, amphetamine in less open, tetrabenazine in fully occluded, and unbound VMAT2 in partially occluded conformations. This structural flexibility facilitates tetrabenazine binding and proton-driven monoamine accumulation. VMAT2 binds serotonin and histamine in opposite orientations through two negatively charged sites, one functioning in protonation. Amphetamine binds in the same pocket without engaging this protonation site. Liposome-based analyses demonstrate that amphetamine directly induces the release of a fluorescent monoamine analog via VMAT2, consistent with an exchange mechanism underlying psychostimulation. These findings reveal the molecular basis of monoamine storage and drug interactions by VMAT2, informing therapeutic development for neurological diseases and substance abuse.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.

Macromolecule Content 

  • Total Structure Weight: 234.93 kDa 
  • Atom Count: 15,303 
  • Modeled Residue Count: 1,905 
  • Deposited Residue Count: 2,056 
  • Unique protein chains: 10

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Synaptic vesicular amine transporter514Homo sapiensMutation(s): 0 
Gene Names: SLC18A2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q05940 (Homo sapiens)
Explore Q05940 
Go to UniProtKB:  Q05940
PHAROS:  Q05940
GTEx:  ENSG00000165646 
Entity Groups
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UniProt GroupQ05940
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1B [auth a]535Komagataella pastorisMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for F2R0K8 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore F2R0K8 
Go to UniProtKB:  F2R0K8
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UniProt GroupF2R0K8
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2C [auth b]236Komagataella pastorisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F2R0J7 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore F2R0J7 
Go to UniProtKB:  F2R0J7
Entity Groups
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UniProt GroupF2R0J7
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3D [auth c]268Komagataella pastorisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F2R0J6 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore F2R0J6 
Go to UniProtKB:  F2R0J6
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UniProt GroupF2R0J6
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4E [auth d]117Komagataella pastorisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F2QT92 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Go to UniProtKB:  F2QT92
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UniProt GroupF2QT92
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5F [auth e]124Komagataella pastorisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F2QVW8 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6G [auth f]100Komagataella pastorisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F2QVA2 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7H [auth g]58Komagataella pastorisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F2QS38 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8I [auth h]48Komagataella pastorisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F2QRE4 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 9J [auth i]56Komagataella pastorisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1G4KPQ9 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore A0A1G4KPQ9 
Go to UniProtKB:  A0A1G4KPQ9
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA
(Subject of Investigation/LOI)

Query on HEA



Download:Ideal Coordinates CCD File
M [auth a],
N [auth a]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PTY
(Subject of Investigation/LOI)

Query on PTY



Download:Ideal Coordinates CCD File
P [auth c],
Q [auth c],
S [auth e],
T [auth i]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
CUA
(Subject of Investigation/LOI)

Query on CUA



Download:Ideal Coordinates CCD File
O [auth b]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
HSM
(Subject of Investigation/LOI)

Query on HSM



Download:Ideal Coordinates CCD File
K [auth A]HISTAMINE
C5 H9 N3
NTYJJOPFIAHURM-UHFFFAOYSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
R [auth d]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
(Subject of Investigation/LOI)

Query on CU



Download:Ideal Coordinates CCD File
L [auth a]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874:
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited StatesEstablished Investigator Award

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Data collection, Database references