6VK9 | pdb_00006vk9

Cryo-EM structure of PilA-N/C from Geobacter sulfurreducens

• PDB DOI: https://doi.org/10.2210/pdb6VK9/pdb
• EM Map EMD-21225: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Geobacter sulfurreducens
• Expression System: Geobacter sulfurreducens
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2020-01-19 Released: 2021-07-07 
• Deposition Author(s): Gu, Y., Srikanth, V., Malvankar, N.S., Samatey, F.A.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Defense (DOD, United States), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Structure of Geobacter pili reveals secretory rather than nanowire behaviour

Gu, Y., Srikanth, V., Salazar-Morales, A.I., Jain, R., O'Brien, P., Yi, S.M., Soni, R.K., Samatey, F.A., Yalcin, S.E., Malvankar, N.S.

(2021) Nature 597: 430-434

• DOI: https://doi.org/10.1038/s41586-021-03857-w

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Hetero 32-mer - A16B16 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 280.8 kDa 
• Atom Count: 19,808 
• Modeled Residue Count: 2,640 
• Deposited Residue Count: 2,640 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geopilin domain 1 protein	A, B [auth O], C [auth Q], D [auth S], E [auth U], F [auth G], G [auth I], H [auth K], I [auth M], J [auth C], K [auth E], L [auth W], M [auth Y], N [auth 0], O [auth 2], P [auth 4]	61	Geobacter sulfurreducens	Mutation(s): 0  Gene Names: pilA-N, GSU1496 Membrane Entity: Yes
UniProt
Find proteins for Q74D23 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74D23  Go to UniProtKB:  Q74D23

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Geopilin domain 2 protein	AA [auth F], BA [auth X], CA [auth Z], DA [auth 1], EA [auth 3], FA [auth 5], Q [auth D], R [auth B], S [auth P], T [auth R], U [auth T], V, W [auth H], X [auth J], Y [auth L], Z [auth N]	104	Geobacter sulfurreducens	Mutation(s): 0  Gene Names: pilA-C, GSU1497 Membrane Entity: Yes
UniProt
Find proteins for Q74D22 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74D22  Go to UniProtKB:  Q74D22

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.05
MODEL REFINEMENT	PHENIX	dev_3689

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Gu, Y., Srikanth, V., Malvankar, N.S., Samatey, F.A.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1749662
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1DP2AI138259-01
Department of Defense (DOD, United States)	United States	W911NF-18-2-0100
National Institutes of Health/Office of the Director	United States	New Innovator Award

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2021-09-01
  Changes: Database references
• Version 1.2: 2021-09-29
  Changes: Database references
• Version 1.3: 2024-05-29
  Changes: Data collection