11YJ | pdb_000011yj

In situ subtomogram average of the transition zone doublet microtubule in human airway cilia (composite map)

  • Classification: STRUCTURAL PROTEIN
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2026-03-18 Released: 2026-09-09 
  • Deposition Author(s): Zhou, H., Brown, A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Richard and Susan Smith Family Foundation, The Giovanni Armenise-Harvard Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.30 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation 3D Report Full Report

Validation slider image for 11YJ

This is version 1.0 of the entry. See complete history. 

Literature

In situ structure of the human ciliary transition zone links linker defects to primary ciliary dyskinesia

Zhou, H., Brown, A.

(2026) Science 

Macromolecule Content 

  • Total Structure Weight: 9,230.84 kDa 
  • Atom Count: 607,834 
  • Modeled Residue Count: 76,471 
  • Deposited Residue Count: 81,535 
  • Unique protein chains: 7

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin alpha-1A chain451Homo sapiensMutation(s): 0 
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q71U36 (Homo sapiens)
Explore Q71U36 
Go to UniProtKB:  Q71U36
PHAROS:  Q71U36
GTEx:  ENSG00000167552 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ71U36
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta-4B chain445Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68371 (Homo sapiens)
Explore P68371 
Go to UniProtKB:  P68371
PHAROS:  P68371
GTEx:  ENSG00000188229 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68371
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 20AF [auth X2],
BF [auth X3],
YE [auth X0],
ZE [auth X1]		193Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6A4 (Homo sapiens)
Explore Q9Y6A4 
Go to UniProtKB:  Q9Y6A4
PHAROS:  Q9Y6A4
GTEx:  ENSG00000070761 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6A4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Centrosomal protein of 41 kDaCF [auth Y0],
DF [auth Y1],
EF [auth Y2]		373Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYV8 (Homo sapiens)
Explore Q9BYV8 
Go to UniProtKB:  Q9BYV8
PHAROS:  Q9BYV8
GTEx:  ENSG00000106477 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYV8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Calcyphosin-like protein208Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWF8 (Homo sapiens)
Explore Q8WWF8 
Go to UniProtKB:  Q8WWF8
PHAROS:  Q8WWF8
GTEx:  ENSG00000152611 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WWF8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Microtubule-associated protein 9AG [auth 9B],
ZF [auth 9A]		647Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q49MG5 (Homo sapiens)
Explore Q49MG5 
Go to UniProtKB:  Q49MG5
PHAROS:  Q49MG5
GTEx:  ENSG00000164114 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ49MG5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Enkurin domain-containing protein 1BG [auth 8A],
CG [auth 8C],
DG [auth 8B]		346Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0I2 (Homo sapiens)
Explore Q9H0I2 
Go to UniProtKB:  Q9H0I2
PHAROS:  Q9H0I2
GTEx:  ENSG00000124074 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H0I2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP


Download:Ideal Coordinates CCD File
AH [auth A2]
AJ [auth I2]
AL [auth P6]
AM [auth T5]
BI [auth E3]
AH [auth A2],
AJ [auth I2],
AL [auth P6],
AM [auth T5],
BI [auth E3],
BK [auth M2],
CH [auth A4],
CJ [auth I4],
CL [auth Q1],
DI [auth E5],
DK [auth M4],
DM [auth U1],
EH [auth A6],
EJ [auth I6],
EL [auth Q3],
FK [auth M6],
FM [auth U3],
GH [auth B1],
GI [auth F1],
GJ [auth J1],
GK [auth N0],
GL [auth Q5],
HM [auth U5],
IH [auth B3],
II [auth F3],
IJ [auth J3],
IK [auth N2],
IL [auth R1],
JM [auth V0],
KH [auth B5],
KI [auth F5],
KJ [auth J5],
KK [auth N4],
KL [auth R3],
LM [auth V2],
MH [auth C1],
MI [auth G0],
MJ [auth K0],
MK [auth N6],
ML [auth R5],
NK [auth O0],
NM [auth V4],
OH [auth C3],
OI [auth G2],
OJ [auth K2],
PK [auth O2],
PL [auth S1],
PM [auth W0],
QH [auth C5],
QI [auth G4],
QJ [auth K4],
RK [auth O4],
RL [auth S3],
RM [auth W2],
SH [auth D1],
SI [auth H0],
SJ [auth L0],
TK [auth O6],
TL [auth S5],
TM [auth W4],
UH [auth D3],
UI [auth H2],
UJ [auth L2],
UK [auth P0],
VM [auth W6],
WH [auth D5],
WI [auth H4],
WJ [auth L4],
WK [auth P1],
WL [auth T1],
YG [auth A0],
YI [auth I0],
YJ [auth L6],
YK [auth P4],
YL [auth T3],
ZH [auth E1],
ZJ [auth M0]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP

Query on GDP


Download:Ideal Coordinates CCD File
AI [auth E2]
AK [auth M1]
BH [auth A3]
BJ [auth I3]
BL [auth Q0]
AI [auth E2],
AK [auth M1],
BH [auth A3],
BJ [auth I3],
BL [auth Q0],
BM [auth T6],
CI [auth E4],
CK [auth M3],
CM [auth U0],
DH [auth A5],
DJ [auth I5],
DL [auth Q2],
EI [auth E6],
EK [auth M5],
EM [auth U2],
FH [auth B0],
FI [auth F0],
FJ [auth J0],
FL [auth Q4],
GM [auth U4],
HH [auth B2],
HI [auth F2],
HJ [auth J2],
HK [auth N1],
HL [auth R0],
IM [auth U6],
JH [auth B4],
JI [auth F4],
JJ [auth J4],
JK [auth N3],
JL [auth R2],
KM [auth V1],
LH [auth C0],
LI [auth F6],
LJ [auth J6],
LK [auth N5],
LL [auth R4],
MM [auth V3],
NH [auth C2],
NI [auth G1],
NJ [auth K1],
NL [auth R6],
OK [auth O1],
OL [auth S0],
OM [auth V5],
PH [auth C4],
PI [auth G3],
PJ [auth K3],
QK [auth O3],
QL [auth S2],
QM [auth W1],
RH [auth D0],
RI [auth G5],
RJ [auth K5],
SK [auth O5],
SL [auth S4],
SM [auth W3],
TH [auth D2],
TI [auth H1],
TJ [auth L1],
UL [auth S6],
UM [auth W5],
VH [auth D4],
VI [auth H3],
VJ [auth L3],
VK [auth P1],
VL [auth T0],
XH [auth D6],
XI [auth H5],
XJ [auth L5],
XK [auth P3],
XL [auth T2],
YH [auth E0],
ZG [auth A1],
ZI [auth I1],
ZK [auth P5],
ZL [auth T4]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.30 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX2.0_5936
RECONSTRUCTIONRELION5

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--
Richard and Susan Smith Family FoundationUnited States--
The Giovanni Armenise-Harvard FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-09
    Type: Initial release