8I7R

In situ structure of axonemal doublet microtubules in mouse sperm with 48-nm repeat

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 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-cell structural insight into the stability of sperm microtubule doublet.

Tai, L., Yin, G., Huang, X., Sun, F., Zhu, Y.

(2023) Cell Discov 9: 116-116

  • DOI: https://doi.org/10.1038/s41421-023-00606-3
  • Primary Citation of Related Structures:  
    8I7O, 8I7R

  • PubMed Abstract: 

    The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. However, the intricate molecular architecture of intact sperm DMT remains elusive. Here, by in situ cryo-electron tomography, we solved the in-cell structure of mouse sperm DMT at 4.5-7.5 Å resolutions, and built its model with 36 kinds of MIPs in 48 nm periodicity. We identified multiple copies of Tektin5 that reinforce Tektin bundle, and multiple MIPs with different periodicities that anchor the Tektin bundle to tubulin wall. This architecture contributes to a superior stability of A-tubule than B-tubule of DMT, which was revealed by structural comparison of DMTs from the intact and deformed axonemes. Our work provides an overall molecular picture of intact sperm DMT in 48 nm periodicity that is essential to understand the molecular mechanism of sperm motility as well as the related ciliopathies.

    • Organizational Affiliation: 

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Meiosis-specific nuclear structural protein 1A,
R [auth B]		491Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-1B [auth A1],
C [auth A2],
D [auth A3],
E [auth A4]		418Mus musculusMutation(s): 0 
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IMPC:  MGI:1333819
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-4B chain
AC [auth DD],
AD [auth EL],
AF [auth GJ],
AH [auth JJ],
AJ [auth ML],
AK [auth OD],
AM [auth RH],
AN [auth TH],
AO [auth VF],
BA [auth BB],
BB [auth CF],
BG [auth IB],
BI [auth LB],
CC [auth DF],
CF [auth GL],
CH [auth JL],
CK [auth OF],
CM [auth RJ],
CN [auth TJ],
CO [auth VH],
DA [auth BD],
DB [auth CH],
DG [auth ID],
DI [auth LD],
EC [auth DH],
EK [auth OH],
EL [auth QB],
EM [auth RL],
EN [auth TL],
EO [auth VJ],
F [auth AB],
FA [auth BF],
FB [auth CJ],
FG [auth IF],
FI [auth LF],
GC [auth DJ],
GK [auth OJ],
GL [auth QD],
GN [auth TN],
GO [auth VL],
H [auth AD],
HA [auth BH],
HB [auth CL],
HG [auth IH],
HI [auth LH],
HM [auth SB],
IC [auth DL],
IJ [auth NB],
IK [auth OL],
IL [auth QF],
J [auth AF],
JA [auth BJ],
JG [auth IJ],
JI [auth LJ],
JM [auth SD],
JN [auth UB],
JO [auth WB],
KH [auth KB],
KJ [auth ND],
KL [auth QH],
L [auth AH],
LA [auth BL],
LF [auth HB],
LG [auth IL],
LI [auth LL],
LM [auth SF],
LN [auth UD],
LO [auth WD],
MD [auth FB],
MH [auth KD],
MJ [auth NF],
ML [auth QJ],
N [auth AJ],
NF [auth HD],
NM [auth SH],
NN [auth UF],
NO [auth WF],
OD [auth FD],
OH [auth KF],
OJ [auth NH],
OK [auth PB],
OL [auth QL],
P [auth AL],
PF [auth HF],
PM [auth SJ],
PN [auth UH],
PO [auth WH],
QC [auth EB],
QD [auth FF],
QH [auth KH],
QI [auth MB],
QJ [auth NJ],
QK [auth PD],
RF [auth HH],
RM [auth SL],
RN [auth UJ],
RO [auth WJ],
SC [auth ED],
SD [auth FH],
SE [auth GB],
SG [auth JB],
SH [auth KJ],
SI [auth MD],
SJ [auth NL],
SK [auth PF],
TF [auth HJ],
TN [auth UL],
TO [auth WL],
UC [auth EF],
UD [auth FJ],
UE [auth GD],
UG [auth JD],
UH [auth KL],
UI [auth MF],
UK [auth PH],
UL [auth RB],
UM [auth TB],
VF [auth HL],
WC [auth EH],
WD [auth FL],
WE [auth GF],
WG [auth JF],
WI [auth MH],
WK [auth PJ],
WL [auth RD],
WM [auth TD],
WN [auth VB],
XA [auth CB],
YB [auth DB],
YC [auth EJ],
YE [auth GH],
YG [auth JH],
YI [auth MJ],
YJ [auth OB],
YK [auth PL],
YL [auth RF],
YM [auth TF],
YN [auth VD],
ZA [auth CD]
427Mus musculusMutation(s): 0 
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IMPC:  MGI:1915472
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Detyrosinated tubulin alpha-3 chain
AB [auth CE],
AG [auth IA],
AI [auth LA],
BC [auth DE],
BF [auth GK],
BH [auth JK],
BJ [auth MM],
BK [auth OE],
BM [auth RI],
BN [auth TI],
BO [auth VG],
CA [auth BC],
CB [auth CG],
CG [auth IC],
CI [auth LC],
DC [auth DG],
DK [auth OG],
DM [auth RK],
DN [auth TK],
DO [auth VI],
EA [auth BE],
EB [auth CI],
EG [auth IE],
EI [auth LE],
FC [auth DI],
FK [auth OI],
FL [auth QC],
FM [auth RM],
FN [auth TM],
FO [auth VK],
G [auth AC],
GA [auth BG],
GB [auth CK],
GG [auth IG],
GI [auth LG],
HC [auth DK],
HJ [auth NA],
HK [auth OK],
HL [auth QE],
I [auth AE],
IA [auth BI],
IB [auth CM],
IG [auth II],
II [auth LI],
IM [auth SC],
IN [auth UA],
IO [auth WA],
JH [auth KA],
JJ [auth NC],
JL [auth QG],
K [auth AG],
KA [auth BK],
KF [auth HA],
KG [auth IK],
KI [auth LK],
KM [auth SE],
KN [auth UC],
KO [auth WC],
LD [auth FA],
LH [auth KC],
LJ [auth NE],
LL [auth QI],
M [auth AI],
MA [auth BM],
MF [auth HC],
MG [auth IM],
MM [auth SG],
MN [auth UE],
MO [auth WE],
ND [auth FC],
NH [auth KE],
NJ [auth NG],
NK [auth PA],
NL [auth QK],
O [auth AK],
OF [auth HE],
OM [auth SI],
ON [auth UG],
OO [auth WG],
PC [auth EA],
PD [auth FE],
PH [auth KG],
PJ [auth NI],
PK [auth PC],
PL [auth QM],
Q [auth AM],
QF [auth HG],
QM [auth SK],
QN [auth UI],
QO [auth WI],
RC [auth EC],
RD [auth FG],
RE [auth GA],
RG [auth JA],
RH [auth KI],
RI [auth MC],
RJ [auth NK],
RK [auth PE],
SF [auth HI],
SM,
SN [auth UK],
SO [auth WK],
TC [auth EE],
TD [auth FI],
TE [auth GC],
TG [auth JC],
TH [auth KK],
TI [auth ME],
TK [auth PG],
UF [auth HK],
VC [auth EG],
VD [auth FK],
VE [auth GE],
VG [auth JE],
VI [auth MG],
VK [auth PI],
VL [auth RC],
VM [auth TC],
VN [auth VA],
XB [auth DA],
XC [auth EI],
XE [auth GG],
XG [auth JG],
XI [auth MI],
XJ [auth OA],
XK [auth PK],
XL [auth RE],
XM [auth TE],
XN [auth VC],
YA [auth CC],
ZB [auth DC],
ZC [auth EK],
ZE [auth GI],
ZG [auth JI],
ZI [auth MK],
ZJ [auth OC],
ZK [auth PM],
ZL [auth RG],
ZM [auth TG],
ZN [auth VE]
438Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-2430Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase 7NA [auth C],
NB [auth D]		395Mus musculusMutation(s): 0 
EC: 2.7.4.6
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IMPC:  MGI:2449121
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-3490Mus musculusMutation(s): 0 
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Find proteins for Q6X6Z7 (Mus musculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-4447Mus musculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain-containing family member BBD [auth F],
KC [auth E]		853Mus musculusMutation(s): 0 
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IMPC:  MGI:3045296
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin bundle-interacting protein 1LC [auth E1],
MC [auth E2],
NC [auth E3],
OC [auth E4]		206Mus musculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Tektin-5557Mus musculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 53DF [auth H],
KE [auth G]		514Mus musculusMutation(s): 0 
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IMPC:  MGI:1921703
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain-containing protein 1LE [auth G1],
ME [auth G2],
NE [auth G3]		648Mus musculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand domain-containing family member C2OE [auth G4],
PE [auth G5],
QE [auth G6]		750Mus musculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAM166A319Mus musculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 95WF [auth I]228Mus musculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAM166CXF [auth I1],
YF [auth I2],
ZF [auth I3]		200Mus musculusMutation(s): 0 
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IMPC:  MGI:1922684
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 107NG [auth J]196Mus musculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity phosphatase 21OG [auth J1],
PG [auth J2],
QG [auth J3]		189Mus musculusMutation(s): 0 
EC: 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 161DH [auth K],
VH [auth L]		303Mus musculusMutation(s): 0 
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IMPC:  MGI:1922806
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 105EH [auth K1],
FH [auth K2],
GH [auth K3],
HH [auth K4],
IH [auth K5]		499Mus musculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
EnkurinWH [auth L1],
XH [auth L2],
YH [auth L3],
ZH [auth L4]		255Mus musculusMutation(s): 0 
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IMPC:  MGI:1918483
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Piercer of microtubule wall 1 proteinMI [auth M]167Mus musculusMutation(s): 0 
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IMPC:  MGI:1916577
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Testis-expressed protein 43NI [auth M1],
OI [auth M2],
PI [auth M3]		141Mus musculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Piercer of microtubule wall 2 proteinCJ [auth N]122Mus musculusMutation(s): 0 
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IMPC:  MGI:3648770
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 276DJ [auth N1],
EJ [auth N2],
FJ [auth N3],
GJ [auth N4]		168Mus musculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RIB43A-like with coiled-coils protein 2AL [auth Q],
JK [auth P],
QL [auth R],
TJ [auth O]		377Mus musculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FlattopUJ [auth O1],
VJ [auth O2],
WJ [auth O3]		189Mus musculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 52KK [auth P1],
LK [auth P2],
MK [auth P3]		620Mus musculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
EF-hand calcium-binding domain-containing protein 6BL [auth Q1],
CL [auth Q2],
DL [auth Q3]		1,516Mus musculusMutation(s): 0 
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IMPC:  MGI:1924877
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia and flagella-associated protein 77RL [auth R1],
SL [auth R2],
TL [auth R3]		283Mus musculusMutation(s): 0 
UniProt
Find proteins for A0A087WRI3 (Mus musculus)
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UniProt GroupA0A087WRI3
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm-associated antigen 8GM [auth S],
TM [auth T]		470Mus musculusMutation(s): 0 
UniProt
Find proteins for Q3V0Q6 (Mus musculus)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 45HN [auth U],
HO [auth W],
UN [auth V],
UO [auth X]		551Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9D9U9 (Mus musculus)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 20193Mus musculusMutation(s): 0 
UniProt
Find proteins for Q8BTU1 (Mus musculus)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Parkin coregulated gene protein homolog241Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DAK2 (Mus musculus)
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IMPC:  MGI:1916560
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 210GQ [auth Z],
IP [auth Y]		547Mus musculusMutation(s): 0 
UniProt
Find proteins for A0JLY1 (Mus musculus)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm acrosome-associated protein 9168Mus musculusMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 141HQ [auth a]101Mus musculusMutation(s): 0 
UniProt
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
AAA [auth UJ]
ABA [auth WL]
AR [auth BH]
AS [auth DI]
AT [auth FK]
AAA [auth UJ],
ABA [auth WL],
AR [auth BH],
AS [auth DI],
AT [auth FK],
AU [auth IA],
AV [auth KB],
AW [auth MD],
AX [auth OF],
AY [auth QH],
AZ [auth SJ],
BAA [auth UK],
BR [auth BI],
BS [auth DJ],
BT [auth FL],
BU [auth IB],
BV [auth KC],
BW [auth MF],
BX [auth OG],
BY [auth QI],
BZ [auth SK],
CAA [auth UL],
CR [auth BJ],
CS [auth DK],
CT [auth GA],
CU [auth IC],
CV [auth KD],
CW [auth MG],
CX [auth OH],
CY [auth QJ],
CZ [auth SL],
DAA [auth VA],
DR [auth BK],
DS [auth DL],
DT [auth GB],
DU [auth ID],
DV [auth KE],
DW [auth MH],
DX [auth OI],
DY [auth QK],
DZ [auth SM],
EAA [auth VB],
ER [auth BL],
ES [auth EA],
ET [auth GC],
EU [auth IE],
EV [auth KF],
EW [auth MI],
EX [auth OJ],
EY [auth QL],
EZ [auth TB],
FAA [auth VC],
FR [auth BM],
FS [auth EB],
FT [auth GD],
FU [auth IF],
FV [auth KG],
FW [auth MJ],
FX [auth OK],
FY [auth QL],
FZ [auth TC],
GAA [auth VD],
GR [auth CB],
GS [auth EC],
GT [auth GE],
GU [auth IG],
GV [auth KH],
GW [auth MK],
GX [auth OL],
GY [auth RB],
GZ [auth TD],
HAA [auth VE],
HR [auth CC],
HS [auth ED],
HT [auth GF],
HU [auth IH],
HV [auth KI],
HW [auth ML],
HX [auth PA],
HY [auth RC],
HZ [auth TE],
IAA [auth VF],
IQ [auth AB],
IR [auth CD],
IS [auth EE],
IT [auth GG],
IU [auth II],
IV [auth KJ],
IW [auth MM],
IX [auth PB],
IY [auth RD],
IZ [auth TF],
JAA [auth VG],
JQ [auth AC],
JR [auth CE],
JS [auth EF],
JT [auth GH],
JU [auth IJ],
JV [auth KK],
JW [auth NA],
JX [auth PC],
JY [auth RE],
JZ [auth TG],
KAA [auth VH],
KQ [auth AD],
KR [auth CF],
KS [auth EG],
KT [auth GI],
KU [auth IK],
KV [auth KL],
KW [auth NB],
KX [auth PD],
KY [auth RF],
KZ [auth TH],
LAA [auth VI],
LQ [auth AE],
LR [auth CG],
LS [auth EH],
LT [auth GJ],
LU [auth IL],
LV [auth LA],
LW [auth NC],
LX [auth PE],
LY [auth RG],
LZ [auth TI],
MAA [auth VJ],
MQ [auth AF],
MR [auth CH],
MS [auth EI],
MT [auth GK],
MU [auth IM],
MV [auth LB],
MW [auth ND],
MX [auth PF],
MY [auth RH],
MZ [auth TJ],
NAA [auth VK],
NQ [auth AG],
NR [auth CI],
NS [auth EJ],
NT [auth GL],
NU [auth JA],
NV [auth LC],
NW [auth NE],
NX [auth PG],
NY [auth RI],
NZ [auth TK],
OAA [auth VL],
OQ [auth AH],
OR [auth CJ],
OS [auth EK],
OT [auth HA],
OU [auth JB],
OV [auth LD],
OW [auth NF],
OX [auth PH],
OY [auth RJ],
OZ [auth TL],
PAA [auth WA],
PQ [auth AI],
PR [auth CK],
PS [auth EL],
PT [auth HB],
PU [auth JC],
PV [auth LE],
PW [auth NG],
PX [auth PI],
PY [auth RK],
PZ [auth TM],
QAA [auth WB],
QQ [auth AJ],
QR [auth CL],
QS [auth FA],
QT [auth HC],
QU [auth JD],
QV [auth LF],
QW [auth NH],
QX [auth PJ],
QY [auth RL],
QZ [auth TN],
RAA [auth WC],
RQ [auth AK],
RR [auth CM],
RS [auth FB],
RT [auth HD],
RU [auth JE],
RV [auth LG],
RW [auth NI],
RX [auth PK],
RY [auth RM],
RZ [auth UA],
SAA [auth WD],
SQ [auth AL],
SR [auth DA],
SS [auth FC],
ST [auth HE],
SU [auth JF],
SV [auth LH],
SW [auth NJ],
SX [auth PL],
SY [auth SB],
SZ [auth UB],
TAA [auth WE],
TQ [auth AM],
TR [auth DB],
TS [auth FD],
TT [auth HF],
TU [auth JG],
TV [auth LI],
TW [auth NK],
TX [auth PM],
TY [auth SC],
TZ [auth UC],
UAA [auth WF],
UQ [auth BB],
UR [auth DC],
US [auth FE],
UT [auth HG],
UU [auth JH],
UV [auth LJ],
UW [auth NL],
UX [auth QB],
UY [auth SD],
UZ [auth UD],
VAA [auth WG],
VQ [auth BC],
VR [auth DD],
VS [auth FF],
VT [auth HH],
VU [auth JI],
VV [auth LK],
VW [auth OA],
VX [auth QC],
VY [auth SE],
VZ [auth UE],
WAA [auth WH],
WQ [auth BD],
WR [auth DE],
WS [auth FG],
WT [auth HI],
WU [auth JJ],
WV [auth LL],
WW [auth OB],
WX [auth QD],
WY [auth SF],
WZ [auth UF],
XAA [auth WI],
XQ [auth BE],
XR [auth DF],
XS [auth FH],
XT [auth HJ],
XU [auth JK],
XV [auth MB],
XW [auth OC],
XX [auth QD],
XY [auth SG],
XZ [auth UG],
YAA [auth WJ],
YQ [auth BF],
YR [auth DG],
YS [auth FI],
YT [auth HK],
YU [auth JL],
YV [auth MC],
YW [auth OD],
YX [auth QF],
YY [auth SH],
YZ [auth UH],
ZAA [auth WK],
ZQ [auth BG],
ZR [auth DH],
ZS [auth FJ],
ZT [auth HL],
ZU [auth KA],
ZV [auth MD],
ZW [auth OE],
ZX [auth QG],
ZY [auth SI],
ZZ [auth UI]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

View Full Validation Report



View more in-depth experimental data
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: 2023-10-11
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references