9IJJ | pdb_00009ijj

In situ structure of the central apparatus in mouse sperm axoneme.

  • Classification: PROTEIN TRANSPORT
  • Organism(s): Mus musculus
  • Mutation(s): No 

  • Deposited: 2024-06-23 Released: 2025-06-04 
  • Deposition Author(s): Zhu, Y., Yin, G., Sun, F.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

In situ structure of the mouse sperm central apparatus reveals mechanistic insights into asthenozoospermia.

Zhu, Y.Lin, T.Yin, G.Tai, L.Chen, L.Ma, J.Huang, G.Lu, Y.Zhang, Z.Wang, B.Chen, S.Sun, F.

(2025) Cell Res 35: 551-567

  • DOI: https://doi.org/10.1038/s41422-025-01135-2
  • Primary Citation of Related Structures:  
    9IJJ

  • PubMed Abstract: 

    The central apparatus (CA) within the sperm axoneme is vital for sperm motility, yet its molecular architecture and functional mechanisms remain incompletely understood. Combining cryo-electron tomography and AlphaFold2, we resolved the in-cell structure of mouse sperm CA at a subnanometer resolution and built a near-complete atomic model. Our analysis identified 39 CA-associated proteins, including eight previously unreported components. By presenting the full-length structures of CFAP47 and HYDIN, we elucidate their molecular roles in tethering the C1 and C2 microtubules within the CA. Specifically, HYDIN forms a semicircular chain that encircles C1 and C2, with its N-terminal half driving the C1-C2 connection and its C-terminal half providing axial support in C2. CFAP47, the core structural component of the bridge, binds C1 through its N-terminal domains, interacts with HYDIN via its central CFAP47-ring, and anchors to C2 through its C-terminal region. The significantly reduced sperm motility and impaired CA structure observed in Cfap47-knockout mice confirmed the important role of CFAP47. Furthermore, genetic analysis of infertile Chinese men with asthenozoospermia identified previously unreported mutations in the CFAP47. The CA structural model elucidates the pathogenic mechanisms of these mutations, establishing a direct link between CFAP47 dysfunction and impaired sperm motility. Therefore, our study provides mechanistic insights into CA-related fertility disorders.


  • Organizational Affiliation
    • National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. zhuyun@ibp.ac.cn.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermatogenesis-associated protein 4295Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein KIF9B [auth c],
C [auth d],
D [auth e],
E [auth f],
F [auth g]
790Mus musculusMutation(s): 0 
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IMPC:  MGI:1098237
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 65G [auth h],
H [auth i],
I [auth j]
1,847Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 701,141Mus musculusMutation(s): 0 
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Find proteins for D3YVL2 (Mus musculus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAM228BO [auth q],
P [auth r],
Q [auth s]
232Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 20R [auth t],
S [auth u]
193Mus musculusMutation(s): 0 
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Find proteins for Q8BTU1 (Mus musculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
MYCBP-associated proteinT [auth v],
U [auth w]
932Mus musculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 46W [auth A],
X [auth B]
2,641Mus musculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 74AA [auth E],
Y [auth C],
Z [auth D]
1,578Mus musculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain containing 180BA [auth F],
CA [auth G]
1,664Mus musculusMutation(s): 0 
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IMPC:  MGI:2685871
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 54DA [auth H],
EA [auth I]
3,106Mus musculusMutation(s): 0 
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Find proteins for Q8C6S9 (Mus musculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 221FA [auth L]836Mus musculusMutation(s): 0 
UniProt
Find proteins for A9Q751 (Mus musculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine rich repeat containing 72GA [auth M]288Mus musculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Deleted in lung and esophageal cancer 1HA [auth O],
IA [auth P]
1,741Mus musculusMutation(s): 0 
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IMPC:  MGI:2443671
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm-associated antigen 16 protein639Mus musculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm-associated antigen 17TA [auth x],
UA [auth y],
VA [auth z]
2,320Mus musculusMutation(s): 0 
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IMPC:  MGI:1921612
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-4B chain
AD [auth Ff],
AE [auth Ib],
AI [auth Ft],
AJ [auth Ip],
BB [auth Af],
BC [auth Db],
BF [auth Kj],
BG [auth Ar],
BH [auth Dn],
BK [auth Kv],
CD [auth Fh],
CE [auth Id],
CI [auth Fv],
CJ [auth Ir],
DB [auth Ah],
DC [auth Dd],
DF [auth Lb],
DG [auth At],
DH [auth Dp],
DK [auth Ln],
ED [auth Fj],
EE [auth If],
EI [auth Fn],
EJ [auth It],
FB [auth Aj],
FC [auth Df],
FF [auth Ld],
FG [auth Av],
FH [auth Dr],
FK [auth Lp],
GD [auth Gb],
GE [auth Ih],
GI [auth Gp],
GJ [auth Iv],
HB [auth Bb],
HC [auth Dh],
HF [auth Lf],
HG [auth Bn],
HH [auth Dt],
HK [auth Lr],
ID [auth Gd],
IE [auth Ij],
II [auth Gr],
IJ [auth In],
JB [auth Bd],
JC [auth Dj],
JF [auth Lh],
JG [auth Bp],
JH [auth Dv],
JK [auth Lt],
KD [auth Gf],
KE [auth Jb],
KI [auth Gt],
KJ [auth Jp],
LB [auth Bf],
LC [auth Eb],
LF [auth Lj],
LG [auth Br],
LH [auth En],
LK [auth Lv],
MD [auth Gh],
ME [auth Jd],
MI [auth Gv],
MJ [auth Jr],
NB [auth Bh],
NC [auth Ed],
NF [auth Mb],
NG [auth Bt],
NH [auth Ep],
NK [auth Mn],
OD [auth Gj],
OE [auth Jf],
OI [auth Gn],
OJ [auth Jt],
PB [auth Bj],
PC [auth Ef],
PF [auth Md],
PG [auth Bv],
PH [auth Er],
PK [auth Mp],
QD [auth Hb],
QE [auth Jh],
QI [auth Hp],
QJ [auth Jv],
RB [auth Cb],
RC [auth Eh],
RF [auth Mf],
RG [auth Cn],
RH [auth Et],
RK [auth Mr],
SD [auth Hd],
SE [auth Jj],
SI [auth Hr],
SJ [auth Jn],
TB [auth Cd],
TC [auth Ej],
TE [auth Kb],
TF [auth Mh],
TG [auth Cp],
TH [auth Ev],
TJ [auth Kn],
TK [auth Mt],
UD [auth Hf],
UI [auth Ht],
VB [auth Cf],
VE [auth Kd],
VF [auth Mj],
VG [auth Cr],
VJ [auth Kp],
VK [auth Mv],
WC [auth Fb],
WD [auth Hh],
WH [auth Fp],
WI [auth Hv],
XA [auth Ab],
XB [auth Ch],
XE [auth Kf],
XF [auth An],
XG [auth Ct],
XJ [auth Kr],
YC [auth Fd],
YD [auth Hj],
YH [auth Fr],
YI [auth Hn],
ZA [auth Ad],
ZB [auth Cj],
ZE [auth Kh],
ZF [auth Ap],
ZG [auth Cv],
ZJ [auth Kt]
445Mus musculusMutation(s): 0 
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IMPC:  MGI:1915472
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-3 chain
AB [auth Ae],
AC [auth Ck],
AF [auth Ki],
AG [auth Aq],
AH [auth Cm],
AK [auth Ku],
BD [auth Fg],
BE [auth Ic],
BI [auth Fu],
BJ [auth Iq],
CB [auth Ag],
CC [auth Dc],
CF [auth Kk],
CG [auth As],
CH [auth Do],
CK [auth Km],
DD [auth Fi],
DE [auth Ie],
DI [auth Fw],
DJ [auth Is],
EB [auth Ai],
EC [auth De],
EF [auth Lc],
EG [auth Au],
EH [auth Dq],
EK [auth Lo],
FD [auth Ga],
FE [auth Ig],
FI [auth Go],
FJ [auth Iu],
GB [auth Ak],
GC [auth Dg],
GF [auth Le],
GG [auth Aw],
GH [auth Ds],
GK [auth Lq],
HD [auth Gc],
HE [auth Ii],
HI [auth Gq],
HJ [auth Iw],
IB [auth Bc],
IC [auth Di],
IF [auth Lg],
IG [auth Bo],
IH [auth Du],
IK [auth Ls],
JD [auth Ge],
JE [auth Ja],
JI [auth Gs],
JJ [auth Jo],
KB [auth Be],
KC [auth Dk],
KF [auth Li],
KG [auth Bq],
KH [auth Dm],
KK [auth Lu],
LD [auth Gg],
LE [auth Jc],
LI [auth Gu],
LJ [auth Jq],
MB [auth Bg],
MC [auth Ec],
MF [auth Lk],
MG [auth Bs],
MH [auth Eo],
MK [auth Lm],
ND [auth Gi],
NE [auth Je],
NI [auth Gw],
NJ [auth Js],
OB [auth Bi],
OC [auth Ee],
OF [auth Mc],
OG [auth Bu],
OH [auth Eq],
OK [auth Mo],
PD [auth Ha],
PE [auth Jg],
PI [auth Ho],
PJ [auth Ju],
QB [auth Bk],
QC [auth Eg],
QF [auth Me],
QG [auth Bm],
QH [auth Es],
QK [auth Mq],
RD [auth Hc],
RE [auth Ji],
RI [auth Hq],
RJ [auth Jw],
SB [auth Cc],
SC [auth Ei],
SF [auth Mg],
SG [auth Co],
SH [auth Eu],
SK [auth Ms],
TD [auth He],
TI [auth Hs],
UB [auth Ce],
UC [auth Ek],
UE [auth Kc],
UF [auth Mi],
UG [auth Cq],
UH [auth Em],
UJ [auth Ko],
UK [auth Mu],
VC [auth Fa],
VD [auth Hg],
VH [auth Fo],
VI [auth Hu],
WB [auth Cg],
WE [auth Ke],
WF [auth Mk],
WG [auth Cs],
WJ [auth Kq],
WK [auth Mm],
XC [auth Fc],
XD [auth Hi],
XH [auth Fq],
XI [auth Hw],
YA [auth Ac],
YB [auth Ci],
YE [auth Kg],
YF [auth Ao],
YG [auth Cu],
YJ [auth Ks],
ZC [auth Fe],
ZD [auth Ia],
ZH [auth Fs],
ZI [auth Io]
450Mus musculusMutation(s): 0 
EC: 3.6.5
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm-associated antigen 6507Mus musculusMutation(s): 0 
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Find proteins for Q9JLI7 (Mus musculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-1149Mus musculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 69AM [auth A3],
BM [auth A4],
ZL [auth A2]
942Mus musculusMutation(s): 0 
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IMPC:  MGI:2443778
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm acrosome-associated protein 9168Mus musculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Protein dpy-30 homolog99Mus musculusMutation(s): 0 
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IMPC:  MGI:1913560
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown1LN [auth 3A]57Mus musculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Spermatogenesis-associated protein 17MN [auth 3B],
TN [auth 3C]
379Mus musculusMutation(s): 0 
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Find proteins for Q9D552 (Mus musculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 119333Mus musculusMutation(s): 0 
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IMPC:  MGI:2685012
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
MORN repeat containing 2CO [auth 3S],
SN [auth 3Q],
ZN [auth 3R]
152Mus musculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown2DO [auth 3Z],
EO [auth 3a]
102Mus musculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown3FO [auth 3b],
GO [auth 3c],
HO [auth 3d]
143Mus musculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown4IO [auth 3e]54Mus musculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown5JO [auth 3f]18Mus musculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown6KO [auth 3g]47Mus musculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella-associated protein 47LO [auth 4A],
MO [auth 4B]
3,184Mus musculusMutation(s): 0 
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IMPC:  MGI:3781475
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrocephalus-inducing proteinNO [auth 4G],
OO [auth 4H],
PO [auth 4I],
QO [auth 4J],
RO [auth 4K]
5,154Mus musculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Germ cell-less protein-like 1SO [auth 4C],
TO [auth 4D],
UO [auth 4E],
VO [auth 4F]
524Mus musculusMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm flagellar protein 2AP [auth 4L],
WO [auth 4M],
YO [auth 4N]
1,724Mus musculusMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat and guanylate kinase domain-containing proteinBP [auth 4O],
XO [auth 4P],
ZO [auth 4Q]
820Mus musculusMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Putative aspartate aminotransferase, cytoplasmic 2404Mus musculusMutation(s): 0 
EC: 2.6.1.1
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat and death domain-containing protein 1IP [auth 4X],
JP [auth 4Y]
853Mus musculusMutation(s): 0 
UniProt
Find proteins for Q8C0R9 (Mus musculus)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
G protein-coupled receptor kinase 3KP [auth 4Z]688Mus musculusMutation(s): 0 
EC: 2.7.11.15
UniProt & NIH Common Fund Data Resources
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IMPC:  MGI:87941
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-gamma catalytic subunitLP [auth 4a]323Mus musculusMutation(s): 0 
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
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IMPC:  MGI:104872
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Microtubule-associated protein 1SIQ [auth 4b],
JQ [auth 4c]
973Mus musculusMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella associated protein 99RQ [auth J],
SQ [auth K],
TQ [auth 5A]
648Mus musculusMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ankyrin repeat and MYND domain-containing protein 1UQ [auth 5B]906Mus musculusMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat-containing protein 43VQ [auth 5C]667Mus musculusMutation(s): 0 
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31925026

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Data collection, Database references