8QQD | pdb_00008qqd

CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus

Gold, V.A.M.Neuhaus, A.Gaines, M.Isupov, M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type IV wide pilus major component PilA4125Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q72JC0 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72JC0 
Go to UniProtKB:  Q72JC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72JC0
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose
BB [auth PA],
BC [auth 5B],
BD [auth lD],
BE [auth RF],
DB [auth XA],
BB [auth PA],
BC [auth 5B],
BD [auth lD],
BE [auth RF],
DB [auth XA],
DC,
DD [auth tD],
DE [auth ZF],
FB [auth fA],
FC [auth LC],
FD [auth 1D],
HB [auth nA],
HC [auth TC],
HD [auth 9D],
JB [auth vA],
JC [auth bC],
JD [auth HE],
LB [auth 3A],
LC [auth jC],
LD [auth PE],
NB [auth BB],
NC [auth rC],
ND [auth XE],
PB [auth JB],
PC [auth zC],
PD [auth fE],
RB,
RC [auth 7C],
RD [auth nE],
TA [auth t],
TB [auth ZB],
TC [auth FD],
TD [auth vE],
VA [auth 1],
VB [auth hB],
VC [auth ND],
VD [auth 3E],
XA [auth 9],
XB [auth pB],
XC [auth VD],
XD [auth BF],
ZA [auth HA],
ZB [auth xB],
ZC [auth dD],
ZD [auth JF]
2O-Glycosylation
Glycosylation Resources
GlyTouCan:  G00039MO
GlyCosmos:  G00039MO
GlyGen:  G00039MO
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
7-Acetamido-5-acetimidoyl-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic aci-(1-4)-alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose
AB [auth KA],
AC [auth 0B],
AD [auth gD],
AE [auth MF],
CB [auth SA],
AB [auth KA],
AC [auth 0B],
AD [auth gD],
AE [auth MF],
CB [auth SA],
CC [auth 8B],
CD [auth oD],
CE [auth UF],
EB [auth aA],
EC [auth GC],
ED [auth wD],
EE [auth cF],
GB [auth iA],
GC [auth OC],
GD [auth 4D],
IB [auth qA],
IC [auth WC],
ID [auth CE],
KB [auth yA],
KC [auth eC],
KD [auth KE],
MB [auth 6A],
MC [auth mC],
MD [auth SE],
OB [auth EB],
OC [auth uC],
OD [auth aE],
QB [auth MB],
QC [auth 2C],
QD [auth iE],
SB [auth UB],
SC [auth AD],
SD [auth qE],
UA [auth w],
UB [auth cB],
UC [auth ID],
UD [auth yE],
WA [auth 4],
WB [auth kB],
WC [auth QD],
WD [auth 6E],
YA [auth CA],
YB [auth sB],
YC [auth YD],
YD [auth EF]
4N/AO-Glycosylation
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A2G
Query on A2G

Download Ideal Coordinates CCD File 
AF [auth J]
AG [auth W]
AH [auth k]
CF [auth K]
CG [auth X]
AF [auth J],
AG [auth W],
AH [auth k],
CF [auth K],
CG [auth X],
CH [auth l],
EF [auth L],
EG [auth Y],
EH [auth m],
GE [auth d],
GF [auth M],
GG [auth Z],
GH [auth n],
IE [auth A],
IF [auth N],
IG [auth a],
IH [auth o],
KE [auth B],
KF [auth O],
KG [auth b],
KH [auth p],
ME [auth C],
MF [auth P],
MG [auth c],
MH [auth q],
OE [auth D],
OF [auth Q],
OG [auth e],
OH [auth r],
QE [auth E],
QF [auth R],
QG [auth f],
QH [auth s],
SE [auth F],
SF [auth S],
SG [auth g],
UE [auth G],
UF [auth T],
UG [auth h],
WE [auth H],
WF [auth U],
WG [auth i],
YE [auth I],
YF [auth V],
YG [auth j]
2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
BF [auth K]
BG [auth X]
BH [auth l]
DF [auth L]
DG [auth Y]
BF [auth K],
BG [auth X],
BH [auth l],
DF [auth L],
DG [auth Y],
DH [auth m],
FE [auth d],
FF [auth M],
FG [auth Z],
FH [auth n],
HE [auth A],
HF [auth N],
HG [auth a],
HH [auth o],
JE [auth B],
JF [auth O],
JG [auth b],
JH [auth p],
LE [auth C],
LF [auth P],
LG [auth c],
LH [auth q],
NE [auth D],
NF [auth Q],
NG [auth e],
NH [auth r],
PE [auth E],
PF [auth R],
PG [auth f],
PH [auth s],
RE [auth F],
RF [auth S],
RG [auth g],
TE [auth G],
TF [auth T],
TG [auth h],
VE [auth H],
VF [auth U],
VG [auth i],
XE [auth I],
XF [auth V],
XG [auth j],
ZE [auth J],
ZF [auth W],
ZG [auth k]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5
RECONSTRUCTIONcryoSPARC4.4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R008639/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection