7OFQ | pdb_00007ofq

The archaellum of Methanocaldococcus villosus

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7OFQ

This is version 1.3 of the entry. See complete history. 

Literature

An archaellum filament composed of two alternating subunits.

Gambelli, L., Isupov, M.N., Conners, R., McLaren, M., Bellack, A., Gold, V., Rachel, R., Daum, B.

(2022) Nat Commun 13: 710-710

  • DOI: https://doi.org/10.1038/s41467-022-28337-1
  • Primary Citation Related Structures: 
    7OFQ

  • PubMed Abstract: 

    Archaea use a molecular machine, called the archaellum, to swim. The archaellum consists of an ATP-powered intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. In many species, several archaellin homologs are encoded in the same operon; however, previous structural studies indicated that archaellum filaments mainly consist of only one protein species. Here, we use electron cryo-microscopy to elucidate the structure of the archaellum from Methanocaldococcus villosus at 3.08 Å resolution. The filament is composed of two alternating archaellins, suggesting that the architecture and assembly of archaella is more complex than previously thought. Moreover, we identify structural elements that may contribute to the filament's flexibility.

    • Organizational Affiliation: 
    • Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.

Macromolecule Content 

  • Total Structure Weight: 999.76 kDa 
  • Atom Count: 80,691 
  • Modeled Residue Count: 9,493 
  • Deposited Residue Count: 9,493 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Archaellin209Methanocaldococcus villosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8X6EH06 (Methanocaldococcus villosus)
Explore A0A8X6EH06 
Go to UniProtKB:  A0A8X6EH06
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8X6EH06
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Archaellin213Methanocaldococcus villosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8X6EH07 (Methanocaldococcus villosus)
Explore A0A8X6EH07 
Go to UniProtKB:  A0A8X6EH07
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8X6EH07
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
(Subject of Investigation/LOI)

Query on CA


Download:Ideal Coordinates CCD File
ADA [auth n]
AK [auth N]
BBA [auth k]
BI [auth K]
CAA [auth j]
ADA [auth n],
AK [auth N],
BBA [auth k],
BI [auth K],
CAA [auth j],
CH [auth J],
DF [auth G],
DY [auth g],
EE [auth F],
EX [auth f],
FC [auth C],
FV [auth c],
GB [auth B],
HS [auth Y],
HU [auth b],
IR [auth X],
JP [auth U],
KO [auth T],
LFA [auth q],
LM [auth Q],
MEA [auth p],
ML [auth P],
NCA [auth m],
NJ [auth M],
OBA [auth l],
OI [auth L],
PG [auth I],
PZ [auth i],
QF [auth H],
QY [auth h],
RD [auth E],
RW [auth e],
SC [auth D],
SV [auth d],
TA [auth A],
TT [auth a],
US [auth Z],
VQ [auth W],
WP [auth V],
XGA [auth s],
XN [auth S],
YFA [auth r],
YM [auth R],
ZDA [auth o],
ZK [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNL(
Subject of Investigation/LOI)

Query on UNL


Download:Ideal Coordinates CCD File
AAA [auth i]
AB [auth A]
ABA [auth j]
AC [auth B]
ACA [auth l]
AAA [auth i],
AB [auth A],
ABA [auth j],
AC [auth B],
ACA [auth l],
AD [auth D],
AE [auth E],
AEA [auth o],
AF [auth F],
AFA [auth p],
AG [auth H],
AGA [auth r],
AH [auth I],
AHA [auth s],
AI [auth J],
AJ [auth L],
AL [auth O],
AM [auth P],
AN [auth R],
AO [auth S],
AP [auth T],
AQ [auth V],
AR [auth W],
AS [auth X],
AT [auth Z],
AU [auth a],
AV [auth b],
AW [auth d],
AX [auth e],
AY [auth f],
AZ [auth h],
BAA [auth i],
BB [auth A],
BC [auth B],
BCA [auth l],
BD [auth D],
BDA [auth n],
BE [auth E],
BEA [auth o],
BF [auth F],
BFA [auth p],
BG [auth H],
BGA [auth r],
BH [auth I],
BHA [auth s],
BJ [auth L],
BK [auth N],
BL [auth O],
BM [auth P],
BN [auth R],
BO [auth S],
BP [auth T],
BQ [auth V],
BR [auth W],
BS [auth X],
BT [auth Z],
BU [auth a],
BV [auth b],
BW [auth d],
BX [auth e],
BY [auth f],
BZ [auth h],
CB [auth A],
CBA [auth k],
CC [auth B],
CCA [auth l],
CD [auth D],
CDA [auth n],
CE [auth E],
CEA [auth o],
CF [auth F],
CFA [auth p],
CG [auth H],
CGA [auth r],
CHA [auth s],
CI [auth K],
CJ [auth L],
CK [auth N],
CL [auth O],
CM [auth P],
CN [auth R],
CO [auth S],
CP [auth T],
CQ [auth V],
CR [auth W],
CS [auth X],
CT [auth Z],
CU [auth a],
CV [auth b],
CW [auth d],
CX [auth e],
CY [auth f],
CZ [auth h],
DAA [auth j],
DB [auth A],
DBA [auth k],
DC [auth B],
DCA [auth l],
DD [auth D],
DDA [auth n],
DE [auth E],
DEA [auth o],
DFA [auth p],
DG [auth H],
DGA [auth r],
DH [auth J],
DHA [auth s],
DI [auth K],
DJ [auth L],
DK [auth N],
DL [auth O],
DM [auth P],
DN [auth R],
DO [auth S],
DP [auth T],
DQ [auth V],
DR [auth W],
DS [auth X],
DT [auth Z],
DU [auth a],
DV [auth b],
DW [auth d],
DX [auth e],
DZ [auth h],
EAA [auth j],
EB [auth A],
EBA [auth k],
EC [auth B],
ECA [auth l],
ED [auth D],
EDA [auth n],
EEA [auth o],
EF [auth G],
EFA [auth p],
EG [auth H],
EGA [auth r],
EH [auth J],
EHA [auth s],
EI [auth K],
EJ [auth L],
EK [auth N],
EL [auth O],
EM [auth P],
EN [auth R],
EO [auth S],
EP [auth T],
EQ [auth V],
ER [auth W],
ES [auth X],
ET [auth Z],
EU [auth a],
EV [auth b],
EW [auth d],
EY [auth g],
EZ [auth h],
FAA [auth j],
FB [auth A],
FBA [auth k],
FCA [auth l],
FD [auth D],
FDA [auth n],
FE [auth F],
FEA [auth o],
FF [auth G],
FFA [auth p],
FG [auth H],
FGA [auth r],
FH [auth J],
FHA [auth s],
FI [auth K],
FJ [auth L],
FK [auth N],
FL [auth O],
FM [auth P],
FN [auth R],
FO [auth S],
FP [auth T],
FQ [auth V],
FR [auth W],
FS [auth X],
FT [auth Z],
FU [auth a],
FW [auth d],
FX [auth f],
FY [auth g],
FZ [auth h],
GAA [auth j],
GBA [auth k],
GC [auth C],
GCA [auth l],
GD [auth D],
GDA [auth n],
GE [auth F],
GEA [auth o],
GF [auth G],
GFA [auth p],
GG [auth H],
GGA [auth r],
GH [auth J],
GHA [auth s],
GI [auth K],
GJ [auth L],
GK [auth N],
GL [auth O],
GM [auth P],
GN [auth R],
GO [auth S],
GP [auth T],
GQ [auth V],
GR [auth W],
GS [auth X],
GT [auth Z],
GU [auth a],
GV [auth c],
GW [auth d],
GX [auth f],
GY [auth g],
GZ [auth h],
HAA [auth j],
HB [auth B],
HBA [auth k],
HC [auth C],
HCA [auth l],
HD [auth D],
HDA [auth n],
HE [auth F],
HEA [auth o],
HF [auth G],
HFA [auth p],
HG [auth H],
HGA [auth r],
HH [auth J],
HHA [auth s],
HI [auth K],
HJ [auth L],
HK [auth N],
HL [auth O],
HM [auth P],
HN [auth R],
HO [auth S],
HP [auth T],
HQ [auth V],
HR [auth W],
HT [auth Z],
HV [auth c],
HW [auth d],
HX [auth f],
HY [auth g],
HZ [auth h],
IAA [auth j],
IB [auth B],
IBA [auth k],
IC [auth C],
ICA [auth l],
ID [auth D],
IDA [auth n],
IE [auth F],
IEA [auth o],
IF [auth G],
IFA [auth p],
IG [auth H],
IGA [auth r],
IH [auth J],
IHA [auth s],
II [auth K],
IJ [auth L],
IK [auth N],
IL [auth O],
IM [auth P],
IN [auth R],
IO [auth S],
IP [auth T],
IQ [auth V],
IS [auth Y],
IT [auth Z],
IU [auth b],
IV [auth c],
IW [auth d],
IX [auth f],
IY [auth g],
IZ [auth h],
JAA [auth j],
JB [auth B],
JBA [auth k],
JC [auth C],
JCA [auth l],
JD [auth D],
JDA [auth n],
JE [auth F],
JEA [auth o],
JF [auth G],
JFA [auth p],
JG [auth H],
JGA [auth r],
JH [auth J],
JHA [auth s],
JI [auth K],
JJ [auth L],
JK [auth N],
JL [auth O],
JM [auth P],
JN [auth R],
JO [auth S],
JQ [auth V],
JR [auth X],
JS [auth Y],
JT [auth Z],
JU [auth b],
JV [auth c],
JW [auth d],
JX [auth f],
JY [auth g],
JZ [auth h],
KAA [auth j],
KB [auth B],
KBA [auth k],
KC [auth C],
KCA [auth l],
KD [auth D],
KDA [auth n],
KE [auth F],
KEA [auth o],
KF [auth G],
KFA [auth p],
KG [auth H],
KGA [auth r],
KH [auth J],
KI [auth K],
KJ [auth L],
KK [auth N],
KL [auth O],
KM [auth P],
KN [auth R],
KP [auth U],
KQ [auth V],
KR [auth X],
KS [auth Y],
KT [auth Z],
KU [auth b],
KV [auth c],
KW [auth d],
KX [auth f],
KY [auth g],
KZ [auth h],
LAA [auth j],
LB [auth B],
LBA [auth k],
LC [auth C],
LCA [auth l],
LD [auth D],
LDA [auth n],
LE [auth F],
LEA [auth o],
LF [auth G],
LG [auth H],
LGA [auth r],
LH [auth J],
LI [auth K],
LJ [auth L],
LK [auth N],
LL [auth O],
LN [auth R],
LO [auth T],
LP [auth U],
LQ [auth V],
LR [auth X],
LS [auth Y],
LT [auth Z],
LU [auth b],
LV [auth c],
LW [auth d],
LX [auth f],
LY [auth g],
LZ [auth h],
MAA [auth j],
MB [auth B],
MBA [auth k],
MC [auth C],
MCA [auth l],
MD [auth D],
MDA [auth n],
ME [auth F],
MF [auth G],
MFA [auth q],
MG [auth H],
MGA [auth r],
MH [auth J],
MI [auth K],
MJ [auth L],
MK [auth N],
MM [auth Q],
MN [auth R],
MO [auth T],
MP [auth U],
MQ [auth V],
MR [auth X],
MS [auth Y],
MT [auth Z],
MU [auth b],
MV [auth c],
MW [auth d],
MX [auth f],
MY [auth g],
MZ [auth h],
NAA [auth j],
NB [auth B],
NBA [auth k],
NC [auth C],
ND [auth D],
NDA [auth n],
NE [auth F],
NEA [auth p],
NF [auth G],
NFA [auth q],
NG [auth H],
NGA [auth r],
NH [auth J],
NI [auth K],
NK [auth N],
NL [auth P],
NM [auth Q],
NN [auth R],
NO [auth T],
NP [auth U],
NQ [auth V],
NR [auth X],
NS [auth Y],
NT [auth Z],
NU [auth b],
NV [auth c],
NW [auth d],
NX [auth f],
NY [auth g],
NZ [auth h],
OAA [auth j],
OB [auth B],
OC [auth C],
OCA [auth m],
OD [auth D],
ODA [auth n],
OE [auth F],
OEA [auth p],
OF [auth G],
OFA [auth q],
OG [auth H],
OGA [auth r],
OH [auth J],
OJ [auth M],
OK [auth N],
OL [auth P],
OM [auth Q],
ON [auth R],
OO [auth T],
OP [auth U],
OQ [auth V],
OR [auth X],
OS [auth Y],
OT [auth Z],
OU [auth b],
OV [auth c],
OW [auth d],
OX [auth f],
OY [auth g],
OZ [auth h],
PAA [auth j],
PB [auth B],
PBA [auth l],
PC [auth C],
PCA [auth m],
PD [auth D],
PDA [auth n],
PE [auth F],
PEA [auth p],
PF [auth G],
PFA [auth q],
PGA [auth r],
PH [auth J],
PI [auth L],
PJ [auth M],
PK [auth N],
PL [auth P],
PM [auth Q],
PN [auth R],
PO [auth T],
PP [auth U],
PQ [auth V],
PR [auth X],
PS [auth Y],
PT [auth Z],
PU [auth b],
PV [auth c],
PW [auth d],
PX [auth f],
PY [auth g],
QAA [auth j],
QB [auth B],
QBA [auth l],
QC [auth C],
QCA [auth m],
QD [auth D],
QDA [auth n],
QE [auth F],
QEA [auth p],
QFA [auth q],
QG [auth I],
QGA [auth r],
QH [auth J],
QI [auth L],
QJ [auth M],
QK [auth N],
QL [auth P],
QM [auth Q],
QN [auth R],
QO [auth T],
QP [auth U],
QQ [auth V],
QR [auth X],
QS [auth Y],
QT [auth Z],
QU [auth b],
QV [auth c],
QW [auth d],
QX [auth f],
QZ [auth i],
RAA [auth j],
RB [auth B],
RBA [auth l],
RC [auth C],
RCA [auth m],
RDA [auth n],
RE [auth F],
REA [auth p],
RF [auth H],
RFA [auth q],
RG [auth I],
RGA [auth r],
RH [auth J],
RI [auth L],
RJ [auth M],
RK [auth N],
RL [auth P],
RM [auth Q],
RN [auth R],
RO [auth T],
RP [auth U],
RQ [auth V],
RR [auth X],
RS [auth Y],
RT [auth Z],
RU [auth b],
RV [auth c],
RX [auth f],
RY [auth h],
RZ [auth i],
SAA [auth j],
SB [auth B],
SBA [auth l],
SCA [auth m],
SD [auth E],
SDA [auth n],
SE [auth F],
SEA [auth p],
SF [auth H],
SFA [auth q],
SG [auth I],
SGA [auth r],
SH [auth J],
SI [auth L],
SJ [auth M],
SK [auth N],
SL [auth P],
SM [auth Q],
SN [auth R],
SO [auth T],
SP [auth U],
SQ [auth V],
SR [auth X],
SS [auth Y],
ST [auth Z],
SU [auth b],
SW [auth e],
SX [auth f],
SY [auth h],
SZ [auth i],
TAA [auth j],
TB [auth B],
TBA [auth l],
TC [auth D],
TCA [auth m],
TD [auth E],
TDA [auth n],
TE [auth F],
TEA [auth p],
TF [auth H],
TFA [auth q],
TG [auth I],
TGA [auth r],
TH [auth J],
TI [auth L],
TJ [auth M],
TK [auth N],
TL [auth P],
TM [auth Q],
TN [auth R],
TO [auth T],
TP [auth U],
TQ [auth V],
TR [auth X],
TS [auth Y],
TU [auth b],
TV [auth d],
TW [auth e],
TX [auth f],
TY [auth h],
TZ [auth i],
UA [auth A],
UAA [auth j],
UB [auth B],
UBA [auth l],
UC [auth D],
UCA [auth m],
UD [auth E],
UDA [auth n],
UE [auth F],
UEA [auth p],
UF [auth H],
UFA [auth q],
UG [auth I],
UGA [auth r],
UH [auth J],
UI [auth L],
UJ [auth M],
UK [auth N],
UL [auth P],
UM [auth Q],
UN [auth R],
UO [auth T],
UP [auth U],
UQ [auth V],
UR [auth X],
UT [auth a],
UU [auth b],
UV [auth d],
UW [auth e],
UX [auth f],
UY [auth h],
UZ [auth i],
VA [auth A],
VAA [auth j],
VB [auth B],
VBA [auth l],
VC [auth D],
VCA [auth m],
VD [auth E],
VDA [auth n],
VE [auth F],
VEA [auth p],
VF [auth H],
VFA [auth q],
VG [auth I],
VGA [auth r],
VH [auth J],
VI [auth L],
VJ [auth M],
VK [auth N],
VL [auth P],
VM [auth Q],
VN [auth R],
VO [auth T],
VP [auth U],
VR [auth X],
VS [auth Z],
VT [auth a],
VU [auth b],
VV [auth d],
VW [auth e],
VX [auth f],
VY [auth h],
VZ [auth i],
WA [auth A],
WAA [auth j],
WB [auth B],
WBA [auth l],
WC [auth D],
WCA [auth m],
WD [auth E],
WDA [auth n],
WE [auth F],
WEA [auth p],
WF [auth H],
WFA [auth q],
WG [auth I],
WGA [auth r],
WH [auth J],
WI [auth L],
WJ [auth M],
WK [auth N],
WL [auth P],
WM [auth Q],
WN [auth R],
WO [auth T],
WQ [auth W],
WR [auth X],
WS [auth Z],
WT [auth a],
WU [auth b],
WV [auth d],
WW [auth e],
WX [auth f],
WY [auth h],
WZ [auth i],
XA [auth A],
XAA [auth j],
XB [auth B],
XBA [auth l],
XC [auth D],
XCA [auth m],
XD [auth E],
XDA [auth n],
XE [auth F],
XEA [auth p],
XF [auth H],
XFA [auth q],
XG [auth I],
XH [auth J],
XI [auth L],
XJ [auth M],
XK [auth N],
XL [auth P],
XM [auth Q],
XO [auth T],
XP [auth V],
XQ [auth W],
XR [auth X],
XS [auth Z],
XT [auth a],
XU [auth b],
XV [auth d],
XW [auth e],
XX [auth f],
XY [auth h],
XZ [auth i],
YA [auth A],
YAA [auth j],
YB [auth B],
YBA [auth l],
YC [auth D],
YCA [auth m],
YD [auth E],
YDA [auth n],
YE [auth F],
YEA [auth p],
YF [auth H],
YG [auth I],
YGA [auth s],
YH [auth J],
YI [auth L],
YJ [auth M],
YK [auth N],
YL [auth P],
YN [auth S],
YO [auth T],
YP [auth V],
YQ [auth W],
YR [auth X],
YS [auth Z],
YT [auth a],
YU [auth b],
YV [auth d],
YW [auth e],
YX [auth f],
YY [auth h],
YZ [auth i],
ZA [auth A],
ZAA [auth j],
ZB [auth B],
ZBA [auth l],
ZC [auth D],
ZCA [auth m],
ZD [auth E],
ZE [auth F],
ZEA [auth p],
ZF [auth H],
ZFA [auth r],
ZG [auth I],
ZGA [auth s],
ZH [auth J],
ZI [auth L],
ZJ [auth M],
ZL [auth P],
ZM [auth R],
ZN [auth S],
ZO [auth T],
ZP [auth V],
ZQ [auth W],
ZR [auth X],
ZS [auth Z],
ZT [auth a],
ZU [auth b],
ZV [auth d],
ZW [auth e],
ZX [auth f],
ZY [auth h],
ZZ [auth i]
Unknown ligand
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.1.0
MODEL REFINEMENTREFMAC5

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)United Kingdom109784

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2025-10-01
    Changes: Advisory, Data collection, Derived calculations, Structure summary