7OFQ

The archaellum of Methanocaldococcus villosus

• PDB DOI: https://doi.org/10.2210/pdb7OFQ/pdb
• EM Map EMD-12875: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Methanocaldococcus villosus
• Expression System: Methanocaldococcus villosus
• Mutation(s): No 


• Deposited: 2021-05-05 Released: 2022-01-19 
• Deposition Author(s): Isupov, M., Gambelli, L., Daum, B.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

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

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

• PubMed: 35132062 
• DOI: https://doi.org/10.1038/s41467-022-28337-1
• Primary Citation of 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.

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Organizational Affiliation: 

Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 45-mer - A23B22 Pseudo Symmetry: Helical - H  (Explore in 3D)
Pseudo Stoichiometry: Homo 45-mer - A45 

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Archaellin	A, AA [auth a], C, CA [auth c], E, EA [auth e], G, GA [auth g], I, IA [auth i], K, KA [auth k], M, MA [auth m], O, OA [auth o], Q, QA [auth q], S, SA [auth s], U, W, Y	209	Methanocaldococcus villosus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Archaellin	B, BA [auth b], D, DA [auth d], F, FA [auth f], H, HA [auth h], J, JA [auth j], L, LA [auth l], N, NA [auth n], P, PA [auth p], R, RA [auth r], T, V, X, Z	213	Methanocaldococcus villosus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	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)	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 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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:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.1.0
MODEL REFINEMENT	REFMAC	5

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-19 
Deposition Author(s): Isupov, M., Gambelli, L., Daum, B.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	United Kingdom	109784

Revision History  

• 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