9H8B | pdb_00009h8b

Ex vivo cannulae fiber structure of Pyrodictium abyssi

• PDB DOI: https://doi.org/10.2210/pdb9H8B/pdb
• EM Map EMD-51935: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Pyrodictium abyssi DSM 6158
• Expression System: Pyrodictium abyssi DSM 6158
• Mutation(s): No 


• Deposited: 2024-10-28 Released: 2024-12-18 
• Deposition Author(s): Sleutel, M., Remaut, H.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Donor Strand Complementation and Calcium Ion Coordination Drive the Chaperone-free Polymerization of Archaeal Cannulae.

Sleutel, M., Sonani, R.R., Miller, J.G., Wang, F., Socorro, A.G., Chen, Y., Martin, R., Demeler, B., Rudolph, M.J., Alva, V., Remaut, H., Egelman, E.H., Conticello, V.P.

(2024) bioRxiv 

• PubMed: 39803462 
• DOI: https://doi.org/10.1101/2024.12.30.630787
• Primary Citation Related Structures: 
  9H8B


• PubMed Abstract: 
  

  Cannulae are tubular protein filaments that accumulate on the extracellular surface of the hyperthermophilic archaeon Pyrodictium abyssi during cell division. Cannulae have been postulated to act as a primitive extracellular matrix through which cells could communicate or exchange material, although their native biological function remains obscure. Here, we report cryoEM structural analyses of ex vivo cannulae and of in vitro protein assemblies derived from recombinant cannula-like proteins. Three-dimensional reconstructions of P. abyssi cannulae revealed that the structural interactions between protomers in the native and recombinant filaments were based on donor strand complementation, a form of non-covalent polymerization in which a donor β-strand from one subunit is inserted into an acceptor groove in a β-sheet of a neighboring subunit. Donor strand complementation in cannulae is reinforced through calcium ion coordination at the interfaces between structural subunits in the respective assemblies. While donor strand complementation occurs during the assembly of chaperone-usher pili, this process requires the participation of accessory proteins that are localized in the outer membrane. In contrast, we demonstrate that calcium ions can induce assembly of cannulae in the absence of other co-factors. Crystallographic analysis of a recombinant cannula-like protein monomer provided evidence that calcium ion binding primes the precursor for donor strand invasion through unblocking of the acceptor groove. Bioinformatic analysis suggested that structurally homologous cannula-like proteins occurred within the genomes of other hyperthermophilic archaea and were encompassed within the TasA superfamily of biomatrix proteins. CryoEM structural analyses of tubular filaments derived from in vitro assembly of a recombinant cannula-like protein from an uncultured Hyperthermus species revealed a common mode of assembly to the Pyrodictium cannulae, in which donor strand complementation and calcium ion binding stabilized longitudinal and lateral assembly in tubular 2D sheets.

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Organizational Affiliation: 
• Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.
Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, Brussels, Belgium.
Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA.
Department of Chemistry, Emory University, Atlanta, GA, 30322, USA.
New York Structural Biology Center, 89 Convent Avenue New York, NY, 10027.
Biochemistry and Molecular Genetics Department, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada.
Department of Protein Evolution, Max Planck Institute for Developmental Biology Tübingen, Tübingen 72076, Germany.
The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 154-mer - A154 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 2,939.37 kDa 
• Atom Count: 179,410 
• Modeled Residue Count: 22,946 
• Deposited Residue Count: 26,796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CanX	A [auth Au], AA [auth BK], AB [auth Bk], AC [auth DQ], AD [auth EG], AE [auth E7], B [auth Av], BA [auth BL], BB [auth Bl], BC [auth DS], BD [auth EI], BE [auth E9], C [auth Aw], CA [auth BM], CB [auth Bm], CC [auth DU], CD [auth EK], CE [auth FA], D [auth Ax], DA [auth BN], DB [auth Bn], DC [auth DW], DD [auth EM], DE [auth FC], E [auth Ay], EA [auth BO], EB [auth Bo], EC [auth DY], ED [auth EO], EE [auth FE], F [auth Az], FA [auth BP], FB [auth Bp], FC [auth Da], FD [auth EQ], FE [auth FG], G [auth A1], GA [auth BQ], GB [auth Bq], GC [auth Dc], GD [auth ES], GE [auth FI], H [auth A2], HA [auth BR], HB [auth Br], HC [auth De], HD [auth EU], HE [auth FK], I [auth A3], IA [auth BS], IB [auth Bs], IC [auth Dg], ID [auth EW], IE [auth FM], J [auth A4], JA [auth BT], JB [auth Bt], JC [auth Di], JD [auth EY], JE [auth FO], K [auth A5], KA [auth BU], KB [auth Bu], KC [auth Dk], KD [auth Ea], KE [auth FQ], L [auth A6], LA [auth BV], LB [auth Bv], LC [auth Dm], LD [auth Ec], LE [auth FS], M [auth A7], MA [auth BW], MB [auth Bw], MC [auth Do], MD [auth Ee], ME [auth FU], N [auth A8], NA [auth BX], NB [auth Bx], NC [auth Dq], ND [auth Eg], NE [auth FW], O [auth A9], OA [auth BY], OB [auth By], OC [auth Ds], OD [auth Ei], OE [auth FY], P [auth A0], PA [auth BZ], PB [auth Bz], PC [auth Du], PD [auth Ek], PE [auth Fa], Q [auth BA], QA [auth Ba], QB [auth B1], QC [auth Dw], QD [auth Em], QE [auth Fc], R [auth BB], RA [auth Bb], RB [auth C9], RC [auth Dy], RD [auth Eo], RE [auth Fe], S [auth BC], SA [auth Bc], SB [auth DA], SC [auth D1], SD [auth Eq], SE [auth Fg], T [auth BD], TA [auth Bd], TB [auth DC], TC [auth D3], TD [auth Es], TE [auth Fi], U [auth BE], UA [auth Be], UB [auth DE], UC [auth D5], UD [auth Eu], UE [auth Fk], V [auth BF], VA [auth Bf], VB [auth DG], VC [auth D7], VD [auth Ew], VE [auth Fm], W [auth BG], WA [auth Bg], WB [auth DI], WC [auth D9], WD [auth Ey], WE [auth Fo], X [auth BH], XA [auth Bh], XB [auth DK], XC [auth EA], XD [auth E1], XE [auth Fq], Y [auth BI], YA [auth Bi], YB [auth DM], YC [auth EC], YD [auth E3], Z [auth BJ], ZA [auth Bj], ZB [auth DO], ZC [auth EE], ZD [auth E5]	174	Pyrodictium abyssi DSM 6158	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	ABA [auth FQ], AM [auth BS], AT [auth DU], AZ [auth Eq], BCA [auth Fi], BI [auth BA], BR [auth Bw], BW [auth D1], BY [auth EQ], CAA [auth FA], CH [auth A6], CK [auth BJ], CN [auth BZ], CO [auth Bg], CP [auth Bm], CS [auth DG], CX [auth EE], CY [auth ES], CZ [auth Es], DBA [auth FS], DJ [auth BF], DM [auth BT], DQ [auth Br], DU [auth Dg], EF [auth Av], EG [auth A1], ER [auth Bx], ES [auth DI], EV [auth Dq], EW [auth D3], EY [auth EU], FAA [auth FC], FCA [auth Fk], FI [auth BB], FN [auth Ba], FO [auth Bh], FZ [auth Eu], GBA [auth FU], GT [auth DW], GX [auth EG], HCA [auth Fm], HK [auth BK], HL [auth BO], HM [auth BU], HP [auth Bn], HQ [auth Bs], HR [auth By], HV [auth Ds], HY [auth EW], IAA [auth FE], IG [auth A2], IH [auth A7], IO [auth Bi], IY [auth EY], IZ [auth Ew], JF [auth Aw], JS [auth DK], JU [auth Di], JW [auth D5], KBA [auth FW], KCA [auth Fo], KN [auth Bb], KR [auth Bz], KS [auth DM], KY [auth Ea], KZ [auth Ey], LAA [auth FG], LH [auth A8], LI [auth BC], LJ [auth BG], LL [auth BP], LM [auth BV], LQ [auth Bt], LT [auth DY], LX [auth EI], MG [auth A3], MP [auth Bo], MW [auth D7], MY [auth Ec], NBA [auth FY], NCA [auth Fq], NF [auth Ax], NK [auth BL], NN [auth Bc], NR [auth B1], NS [auth DO], NU [auth Dk], NV [auth Du], NZ [auth E1], OAA [auth FI], OX [auth EK], PBA [auth Fa], PJ [auth BH], PM [auth BW], PO [auth Bj], PT [auth Da], PY [auth Ee], QS [auth DQ], QW [auth D9], RH [auth A9], RL [auth BQ], RN [auth Bd], RR [auth C9], RY [auth Eg], RZ [auth E3], SAA [auth FK], SG [auth A4], SI [auth BD], SP [auth Bp], SQ [auth Bu], SR [auth DA], SY [auth Ei], TBA [auth Fc], TK [auth BM], TO [auth Bk], TT [auth Dc], TV [auth Dw], TX [auth EM], UF [auth Ay], UM [auth BX], US [auth DS], UU [auth Dm], UW [auth EA], UZ [auth E5], VAA [auth FM], VJ [auth BI], VN [auth Be], VQ [auth Bv], VY [auth Ek], WBA [auth Fe], WL [auth BR], WX [auth EO], WY [auth Em], WZ [auth E7], XG [auth A5], XH [auth A0], XM [auth BY], XR [auth DC], XU [auth Do], XV [auth Dy], YAA [auth FO], YI [auth BE], YN [auth Bf], YO [auth Bl], YP [auth Bq], YR [auth DE], YT [auth De], YW [auth EC], YY [auth Eo], ZBA [auth Fg], ZE [auth Au], ZF [auth Az], ZK [auth BN], ZZ [auth E9]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	AAA [auth E9], ACA [auth Fg], AF [auth Au], AG [auth Az], AH [auth A5], AI [auth BA], AJ [auth BE], AK [auth BI], AL [auth BN], AN [auth BY], AO [auth Bf], AP [auth Bl], AQ [auth Bq], AR [auth Bw], AS [auth DE], AU [auth De], AV [auth Do], AW [auth D1], AX [auth EC], AY [auth EQ], BAA [auth E9], BBA [auth FQ], BF [auth Au], BG [auth Az], BH [auth A6], BJ [auth BE], BK [auth BJ], BL [auth BN], BM [auth BS], BN [auth BZ], BO [auth Bg], BP [auth Bl], BQ [auth Br], BS [auth DG], BT [auth DU], BU [auth De], BV [auth Do], BX [auth EC], BZ [auth Eq], CBA [auth FQ], CCA [auth Fi], CF [auth Au], CG [auth A1], CI [auth BA], CJ [auth BE], CL [auth BN], CM [auth BS], CQ [auth Br], CR [auth Bw], CT [auth DU], CU [auth De], CV [auth Dq], CW [auth D1], DAA [auth FA], DCA [auth Fi], DF [auth Av], DG [auth A1], DH [auth A6], DI [auth BA], DK [auth BJ], DL [auth BN], DN [auth BZ], DO [auth Bg], DP [auth Bm], DR [auth Bx], DS [auth DG], DT [auth DU], DV [auth Dq], DW [auth D1], DX [auth EE], DY [auth ES], DZ [auth Es], EAA [auth FA], EBA [auth FS], ECA [auth Fk], EH [auth A6], EI [auth BA], EJ [auth BF], EK [auth BJ], EL [auth BN], EM [auth BT], EN [auth BZ], EO [auth Bh], EP [auth Bm], EQ [auth Br], ET [auth DW], EU [auth Dg], EX [auth EE], EZ [auth Eu], FBA [auth FS], FF [auth Av], FG [auth A1], FH [auth A6], FJ [auth BF], FK [auth BJ], FL [auth BO], FM [auth BT], FP [auth Bm], FQ [auth Br], FR [auth Bx], FS [auth DI], FT [auth DW], FU [auth Dg], FV [auth Dq], FW [auth D3], FX [auth EE], FY [auth EU], GAA [auth FC], GCA [auth Fk], GF [auth Av], GG [auth A1], GH [auth A7], GI [auth BB], GJ [auth BF], GK [auth BJ], GL [auth BO], GM [auth BT], GN [auth Ba], GO [auth Bh], GP [auth Bm], GQ [auth Bs], GR [auth By], GS [auth DI], GU [auth Dg], GV [auth Dq], GW [auth D3], GY [auth EW], GZ [auth Eu], HAA [auth FC], HBA [auth FU], HF [auth Av], HG [auth A2], HH [auth A7], HI [auth BB], HJ [auth BF], HN [auth Ba], HO [auth Bh], HS [auth DK], HT [auth DW], HU [auth Dg], HW [auth D3], HX [auth EG], HZ [auth Ew], IBA [auth FU], ICA [auth Fm], IF [auth Aw], II [auth BB], IJ [auth BF], IK [auth BK], IL [auth BO], IM [auth BU], IN [auth Ba], IP [auth Bn], IQ [auth Bs], IR [auth By], IS [auth DK], IT [auth DW], IU [auth Di], IV [auth Ds], IW [auth D5], IX [auth EG], JAA [auth FE], JBA [auth FW], JCA [auth Fm], JG [auth A2], JH [auth A7], JI [auth BB], JJ [auth BG], JK [auth BK], JL [auth BO], JM [auth BU], JN [auth Bb], JO [auth Bi], JP [auth Bn], JQ [auth Bs], JR [auth Bz], JT [auth DY], JV [auth Ds], JX [auth EG], JY [auth EY], JZ [auth Ew], KAA [auth FE], KF [auth Aw], KG [auth A2], KH [auth A7], KI [auth BB], KJ [auth BG], KK [auth BK], KL [auth BO], KM [auth BU], KO [auth Bi], KP [auth Bn], KQ [auth Bs], KT [auth DY], KU [auth Di], KV [auth Ds], KW [auth D5], KX [auth EI], LBA [auth FW], LCA [auth Fo], LF [auth Aw], LG [auth A2], LK [auth BK], LN [auth Bb], LO [auth Bi], LP [auth Bn], LR [auth Bz], LS [auth DM], LU [auth Di], LV [auth Ds], LW [auth D5], LY [auth Ea], LZ [auth Ey], MAA [auth FG], MBA [auth FY], MCA [auth Fo], MF [auth Aw], MH [auth A8], MI [auth BC], MJ [auth BG], MK [auth BK], ML [auth BP], MM [auth BV], MN [auth Bb], MO [auth Bi], MQ [auth Bt], MR [auth B1], MS [auth DM], MT [auth DY], MU [auth Di], MV [auth Du], MX [auth EI], MZ [auth Ey], NAA [auth FG], NG [auth A3], NH [auth A8], NI [auth BC], NJ [auth BG], NL [auth BP], NM [auth BV], NO [auth Bj], NP [auth Bo], NQ [auth Bt], NT [auth DY], NW [auth D7], NX [auth EI], NY [auth Ec], OBA [auth FY], OCA [auth Fq], OF [auth Ax], OG [auth A3], OH [auth A8], OI [auth BC], OJ [auth BG], OK [auth BL], OL [auth BP], OM [auth BV], ON [auth Bc], OO [auth Bj], OP [auth Bo], OQ [auth Bt], OR [auth B1], OS [auth DO], OT [auth Da], OU [auth Dk], OV [auth Du], OW [auth D7], OY [auth Ee], OZ [auth E1], PAA [auth FI], PCA [auth Fq], PF [auth Ax], PG [auth A3], PH [auth A8], PI [auth BC], PK [auth BL], PL [auth BP], PN [auth Bc], PP [auth Bo], PQ [auth Bt], PR [auth C9], PS [auth DO], PU [auth Dk], PV [auth Du], PW [auth D7], PX [auth EK], PZ [auth E1], QAA [auth FI], QBA [auth Fa], QF [auth Ax], QG [auth A3], QH [auth A9], QI [auth BC], QJ [auth BH], QK [auth BL], QL [auth BP], QM [auth BW], QN [auth Bc], QO [auth Bj], QP [auth Bo], QQ [auth Bu], QR [auth C9], QT [auth Da], QU [auth Dk], QV [auth Du], QX [auth EK], QY [auth Eg], QZ [auth E3], RAA [auth FK], RBA [auth Fa], RF [auth Ax], RG [auth A4], RI [auth BD], RJ [auth BH], RK [auth BL], RM [auth BW], RO [auth Bj], RP [auth Bp], RQ [auth Bu], RS [auth DQ], RT [auth Da], RU [auth Dk], RV [auth Dw], RW [auth D9], RX [auth EK], SBA [auth Fc], SF [auth Ay], SH [auth A9], SJ [auth BH], SK [auth BL], SL [auth BQ], SM [auth BW], SN [auth Bd], SO [auth Bk], SS [auth DQ], ST [auth Da], SU [auth Dm], SV [auth Dw], SW [auth D9], SX [auth EM], SZ [auth E3], TAA [auth FK], TF [auth Ay], TG [auth A4], TH [auth A9], TI [auth BD], TJ [auth BH], TL [auth BQ], TM [auth BX], TN [auth Bd], TP [auth Bp], TQ [auth Bu], TR [auth DA], TS [auth DQ], TU [auth Dm], TW [auth D9], TY [auth Ei], TZ [auth E5], UAA [auth FM], UBA [auth Fc], UG [auth A4], UH [auth A9], UI [auth BD], UJ [auth BH], UK [auth BM], UL [auth BQ], UN [auth Bd], UO [auth Bk], UP [auth Bp], UQ [auth Bu], UR [auth DA], UT [auth Dc], UV [auth Dw], UX [auth EM], UY [auth Ek], VBA [auth Fe], VF [auth Ay], VG [auth A4], VH [auth A0], VI [auth BD], VK [auth BM], VL [auth BR], VM [auth BX], VO [auth Bk], VP [auth Bp], VR [auth DC], VS [auth DS], VT [auth Dc], VU [auth Dm], VV [auth Dw], VW [auth EA], VX [auth EM], VZ [auth E5], WAA [auth FM], WF [auth Ay], WG [auth A5], WH [auth A0], WI [auth BD], WJ [auth BI], WK [auth BM], WM [auth BX], WN [auth Be], WO [auth Bk], WP [auth Bq], WQ [auth Bv], WR [auth DC], WS [auth DS], WT [auth Dc], WU [auth Dm], WV [auth Dy], WW [auth EA], XAA [auth FO], XBA [auth Fe], XF [auth Az], XI [auth BE], XJ [auth BI], XK [auth BM], XL [auth BR], XN [auth Be], XO [auth Bl], XP [auth Bq], XQ [auth Bv], XS [auth DS], XT [auth Dc], XW [auth EA], XX [auth EO], XY [auth Em], XZ [auth E7], YBA [auth Fg], YE [auth Au], YF [auth Az], YG [auth A5], YH [auth A0], YJ [auth BI], YK [auth BM], YL [auth BR], YM [auth BY], YQ [auth Bv], YS [auth DS], YU [auth Do], YV [auth Dy], YX [auth EO], YZ [auth E7], ZAA [auth FO], ZG [auth A5], ZH [auth A0], ZI [auth BE], ZJ [auth BI], ZL [auth BS], ZM [auth BY], ZN [auth Bf], ZO [auth Bl], ZP [auth Bq], ZQ [auth Bv], ZR [auth DE], ZS [auth DU], ZT [auth De], ZU [auth Do], ZV [auth Dy], ZW [auth EC], ZX [auth EO], ZY [auth Eo]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Sleutel, M., Remaut, H.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G043021N

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Data collection, Database references