7UN1

8-nm repeat of the human sperm tip singlet microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules.

Gui, M.Croft, J.T.Zabeo, D.Acharya, V.Kollman, J.M.Burgoyne, T.Hoog, J.L.Brown, A.

(2022) Proc Natl Acad Sci U S A 119: e2207605119-e2207605119

  • DOI: https://doi.org/10.1073/pnas.2207605119
  • Primary Citation of Related Structures:  
    7UN1, 7UNG

  • PubMed Abstract: 

    The cilium-centrosome complex contains triplet, doublet, and singlet microtubules. The lumenal surfaces of each microtubule within this diverse array are decorated by microtubule inner proteins (MIPs). Here, we used single-particle cryo-electron microscopy methods to build atomic models of two types of human ciliary microtubule: the doublet microtubules of multiciliated respiratory cells and the distal singlet microtubules of monoflagellated human spermatozoa. We discover that SPACA9 is a polyspecific MIP capable of binding both microtubule types. SPACA9 forms intralumenal striations in the B tubule of respiratory doublet microtubules and noncontinuous spirals in sperm singlet microtubules. By acquiring new and reanalyzing previous cryo-electron tomography data, we show that SPACA9-like intralumenal striations are common features of different microtubule types in animal cilia. Our structures provide detailed references to help rationalize ciliopathy-causing mutations and position cryo-EM as a tool for the analysis of samples obtained directly from ciliopathy patients.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm acrosome-associated protein 9222Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96E40 (Homo sapiens)
Explore Q96E40 
Go to UniProtKB:  Q96E40
PHAROS:  Q96E40
GTEx:  ENSG00000165698 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96E40
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  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:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1A chain451Homo sapiensMutation(s): 0 
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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
AG [auth IE]
AH [auth LC]
CE [auth CG]
CF [auth FG]
DG [auth IG]
AG [auth IE],
AH [auth LC],
CE [auth CG],
CF [auth FG],
DG [auth IG],
DH [auth LE],
FE [auth DC],
FF [auth GC],
GD [auth AC],
GG [auth JC],
GH [auth MA],
IE [auth DE],
IF [auth GE],
JD [auth AE],
JG [auth JE],
JH [auth MC],
LE [auth DG],
LF [auth GG],
MG [auth JG],
MH [auth ME],
ND [auth BC],
OE [auth EC],
OF [auth HC],
OG [auth KC],
QD [auth BE],
RE [auth EE],
RF [auth HE],
RG [auth KE],
TD [auth BG],
UE [auth EG],
UF [auth HG],
UG [auth KG],
WD [auth CC],
WE [auth FC],
XF [auth IC],
XG [auth LA],
ZD [auth CE],
ZE [auth FE]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
BE [auth CF]
BF [auth FF]
CG [auth IF]
CH [auth LD]
EE [auth DB]
BE [auth CF],
BF [auth FF],
CG [auth IF],
CH [auth LD],
EE [auth DB],
EF [auth FH],
FD [auth AB],
FG [auth IH],
FH [auth LF],
HE [auth DD],
HF [auth GD],
ID [auth AD],
IG [auth JD],
IH [auth MB],
KE [auth DF],
KF [auth GF],
LD [auth AF],
LG [auth JF],
LH [auth MD],
MD [auth BA],
NE [auth EB],
NF [auth GH],
OH [auth MF],
PD [auth BD],
QE [auth ED],
QF [auth HD],
QG [auth KD],
SD [auth BF],
TE [auth EF],
TF [auth HF],
TG [auth KF],
VD [auth CB],
WF [auth HH],
WG [auth KH],
YD [auth CD],
YE [auth FD],
ZF [auth ID],
ZG [auth LB]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth CE]
AF [auth FE]
BG [auth IE]
BH [auth LC]
DE [auth CG]
AE [auth CE],
AF [auth FE],
BG [auth IE],
BH [auth LC],
DE [auth CG],
DF [auth FG],
EG [auth IG],
EH [auth LE],
GE [auth DC],
GF [auth GC],
HD [auth AC],
HG [auth JC],
HH [auth MA],
JE [auth DE],
JF [auth GE],
KD [auth AE],
KG [auth JE],
KH [auth MC],
ME [auth DG],
MF [auth GG],
NG [auth JG],
NH [auth ME],
OD [auth BC],
PE [auth EC],
PF [auth HC],
PG [auth KC],
RD [auth BE],
SE [auth EE],
SF [auth HE],
SG [auth KE],
UD [auth BG],
VE [auth EG],
VF [auth HG],
VG [auth KG],
XD [auth CC],
XE [auth FC],
YF [auth IC],
YG [auth LA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM141109
Swedish Research CouncilSweden2015-05427
Swedish Research CouncilSweden2019-04004
Smith Family FoundationUnited States--
Pew Charitable TrustsUnited States--
Charles A. King Trust Postdoctoral Research FellowshipUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2022-10-19
    Changes: Database references