8C8R

In situ structure of the Nitrosopumilus maritimus S-layer - Composite map between C2 and C6

PDB DOI: https://doi.org/10.2210/pdb8C8R/pdb
EM Map EMD-16492: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Nitrosopumilus maritimus SCM1
Mutation(s): No

Deposited: 2023-01-20 Released: 2024-04-17
Deposition Author(s): von Kuegelgen, A., Bharat, T.
Funding Organization(s): Wellcome Trust, Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: CELL
Reconstruction Method: SUBTOMOGRAM AVERAGING

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Membraneless channels sieve cations in ammonia-oxidizing marine archaea

von Kuegelgen, A., Cassidy, C.K., van Dorst, S., Pagani, L.L., Ford, Z., Loewe, J., Stansfeld, P.J., Bharat, T.A.M.

(2024) Nature

DOI: https://doi.org/10.1038/s41586-024-07462-5

Macromolecule Content

Total Structure Weight: 1,098.94 kDa
Atom Count: 65,154
Modelled Residue Count: 8,772
Deposited Residue Count: 10,404
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell surface protein	A, B, C, D, E A, B, C, D, E, F	1,734	Nitrosopumilus maritimus SCM1	Mutation(s): 0
UniProt
Find proteins for A9A4Y9 (Nitrosopumilus maritimus (strain SCM1)) Explore A9A4Y9 Go to UniProtKB: A9A4Y9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9A4Y9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: CELL
Reconstruction Method: SUBTOMOGRAM AVERAGING

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0.0
MODEL REFINEMENT	PHENIX	1.19-4092
MODEL REFINEMENT	REFMAC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

von Kuegelgen, A.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	202231/Z/16/Z
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_1201/31

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release
Version 1.1: 2024-06-05
Changes: Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.