9YGU | pdb_00009ygu

Flagella filament structure in H. pylori composed of flagellin FlaA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Assembly and glycosylation of Helicobacter pylori sheathed flagella.

Kumar, R.Tachiyama, S.Yu, H.Heydari, S.Guo, J.Botting, J.M.Guo, W.Hoover, T.R.Liu, J.

(2026) PNAS Nexus 5: pgag011-pgag011

  • DOI: https://doi.org/10.1093/pnasnexus/pgag011
  • Primary Citation of Related Structures:  
    9YGU, 9YH1

  • PubMed Abstract: 

    The bacterial flagellum is a complex nanomachine essential for motility, colonization, and invasion in diverse species. Helicobacter pylori has evolved elaborate sheathed flagella that enable migration through the highly viscous gastric mucus layer to reach its colonization niche on the gastric epithelium, yet the molecular basis for these unique adaptations has remained elusive. Here, we use in situ single-particle cryo-electron microscopy to determine near-atomic structures of the flagellar filament within the membranous sheath of H. pylori . The major flagellin FlaA constitutes the bulk of the filament, whereas the minor flagellin FlaB contributes critically to the hook-proximal region. Both FlaA and FlaB form a conserved core surrounded by variable surface-exposed domains. Our structures further reveal that pseudaminic acid glycans decorate these domains, where they mediate inter- and intra-subunit contacts that stabilize the filament and confer a negatively charged surface. Together, these findings support a model in which the filament rotates independently of the membranous sheath to drive H. pylori motility and provide a molecular framework for understanding how the sheathed flagellum enables colonization and persistence within the gastric niche.


  • Organizational Affiliation
    • Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flagellin508Helicobacter pylori B128Mutation(s): 0 
UniProt
Find proteins for B8Q9B9 (Helicobacter pylori)
Explore B8Q9B9 
Go to UniProtKB:  B8Q9B9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8Q9B9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P8E
Query on P8E

Download Ideal Coordinates CCD File 
AB [auth I3]
AC [auth A7]
AD [auth FB]
AE [auth KE]
AF [auth NI]
AB [auth I3],
AC [auth A7],
AD [auth FB],
AE [auth KE],
AF [auth NI],
AG [auth XM],
AH [auth GQ],
AI [auth CT],
AJ [auth EX],
BB [auth I3],
BC [auth A7],
BD [auth FB],
BE [auth LF],
BF [auth NI],
BG [auth XM],
BH [auth GQ],
BI [auth CT],
BJ [auth EX],
CB [auth R4],
CC [auth A7],
CD [auth FB],
CE [auth LF],
CF [auth NI],
CG [auth XM],
CH [auth GQ],
CI [auth PU],
CJ [auth EX],
DB [auth R4],
DC [auth A7],
DD [auth FB],
DE [auth LF],
DF [auth BJ],
DG [auth XM],
DH [auth GQ],
DI [auth PU],
DJ [auth EX],
EB [auth R4],
EC [auth e8],
ED [auth FB],
EE [auth LF],
EF [auth BJ],
EG [auth XM],
EH [auth GQ],
EI [auth PU],
FB [auth R4],
FC [auth e8],
FD [auth FB],
FE [auth LF],
FF [auth BJ],
FG [auth DN],
FH [auth GQ],
FI [auth PU],
GB [auth R4],
GC [auth e8],
GD [auth dC],
GE [auth LF],
GF [auth BJ],
GG [auth DN],
GH [auth GQ],
GI [auth PU],
HA [auth Y1],
HB [auth R4],
HC [auth e8],
HD [auth dC],
HE [auth LF],
HF [auth BJ],
HG [auth DN],
HH [auth VR],
HI [auth PU],
IA [auth Y1],
IB [auth R4],
IC [auth e8],
ID [auth dC],
IE [auth WG],
IF [auth BJ],
IG [auth DN],
IH [auth VR],
II [auth PU],
JA [auth Y1],
JB [auth S5],
JC [auth e8],
JD [auth dC],
JE [auth WG],
JF [auth BJ],
JG [auth DN],
JH [auth VR],
JI [auth cV],
KA [auth Y1],
KB [auth S5],
KC [auth e8],
KD [auth dC],
KE [auth WG],
KF [auth fK],
KG [auth DN],
KH [auth VR],
KI [auth cV],
LA [auth Y1],
LB [auth S5],
LC [auth Z9],
LD [auth dC],
LE [auth WG],
LF [auth fK],
LG [auth DN],
LH [auth VR],
LI [auth cV],
MA [auth Y1],
MB [auth S5],
MC [auth Z9],
MD [auth dC],
ME [auth WG],
MF [auth fK],
MG [auth MO],
MH [auth VR],
MI [auth cV],
NA [auth Y1],
NB [auth S5],
NC [auth Z9],
ND [auth JD],
NE [auth WG],
NF [auth fK],
NG [auth MO],
NH [auth VR],
NI [auth cV],
OA [auth Q2],
OB [auth S5],
OC [auth Z9],
OD [auth JD],
OE [auth WG],
OF [auth fK],
OG [auth MO],
OH [auth bS],
OI [auth cV],
PA [auth Q2],
PB [auth S5],
PC [auth Z9],
PD [auth JD],
PE [auth UH],
PF [auth fK],
PG [auth MO],
PH [auth bS],
PI [auth cV],
QA [auth Q2],
QB [auth g6],
QC [auth Z9],
QD [auth JD],
QE [auth UH],
QF [auth fK],
QG [auth MO],
QH [auth bS],
QI [auth aW],
RA [auth Q2],
RB [auth g6],
RC [auth Z9],
RD [auth JD],
RE [auth UH],
RF [auth HL],
RG [auth MO],
RH [auth bS],
RI [auth aW],
SA [auth Q2],
SB [auth g6],
SC [auth OA],
SD [auth JD],
SE [auth UH],
SF [auth HL],
SG [auth MO],
SH [auth bS],
SI [auth aW],
TA [auth Q2],
TB [auth g6],
TC [auth OA],
TD [auth JD],
TE [auth UH],
TF [auth HL],
TG [auth TP],
TH [auth bS],
TI [auth aW],
UA [auth Q2],
UB [auth g6],
UC [auth OA],
UD [auth KE],
UE [auth UH],
UF [auth HL],
UG [auth TP],
UH [auth bS],
UI [auth aW],
VA [auth I3],
VB [auth g6],
VC [auth OA],
VD [auth KE],
VE [auth UH],
VF [auth HL],
VG [auth TP],
VH [auth CT],
VI [auth aW],
WA [auth I3],
WB [auth g6],
WC [auth OA],
WD [auth KE],
WE [auth NI],
WF [auth HL],
WG [auth TP],
WH [auth CT],
WI [auth aW],
XA [auth I3],
XB [auth A7],
XC [auth OA],
XD [auth KE],
XE [auth NI],
XF [auth HL],
XG [auth TP],
XH [auth CT],
XI [auth EX],
YA [auth I3],
YB [auth A7],
YC [auth OA],
YD [auth KE],
YE [auth NI],
YF [auth XM],
YG [auth TP],
YH [auth CT],
YI [auth EX],
ZA [auth I3],
ZB [auth A7],
ZC [auth FB],
ZD [auth KE],
ZE [auth NI],
ZF [auth XM],
ZG [auth TP],
ZH [auth CT],
ZI [auth EX]
5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid
C9 H18 N2 O6
ZFZFJUIKYIVPNP-YXGHPGITSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited States1S10 OD023603-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-25
    Type: Initial release