5ZRT | pdb_00005zrt

Crystal structure of human C1ORF123 protein

• PDB DOI: https://doi.org/10.2210/pdb5ZRT/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-25 Released: 2018-08-01 
• Deposition Author(s): Rahaman, S.N.A., Yusop, J.M., Mohamed-Hussein, Z.A., Wan Mohd, A., Ho, K.L., Teh, A.H., Waterman, J., Ng, C.L.
• Funding Organization(s): Ministry of Science, Technology and Innovation (Malaysia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.220 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal structure and functional analysis of human C1ORF123.

A Rahaman, S.N., Mat Yusop, J., Mohamed-Hussein, Z.A., Aizat, W.M., Ho, K.L., Teh, A.H., Waterman, J., Tan, B.K., Tan, H.L., Li, A.Y., Chen, E.S., Ng, C.L.

(2018) PeerJ 6: e5377-e5377

• PubMed: 30280012 
• DOI: https://doi.org/10.7717/peerj.5377
• Primary Citation Related Structures: 
  5ZRT


• PubMed Abstract: 
  

  Proteins of the DUF866 superfamily are exclusively found in eukaryotic cells. A member of the DUF866 superfamily, C1ORF123, is a human protein found in the open reading frame 123 of chromosome 1. The physiological role of C1ORF123 is yet to be determined. The only available protein structure of the DUF866 family shares just 26% sequence similarity and does not contain a zinc binding motif. Here, we present the crystal structure of the recombinant human C1ORF123 protein (rC1ORF123). The structure has a 2-fold internal symmetry dividing the monomeric protein into two mirrored halves that comprise of distinct electrostatic potential. The N-terminal half of rC1ORF123 includes a zinc-binding domain interacting with a zinc ion near to a potential ligand binding cavity. Functional studies of human C1ORF123 and its homologue in the fission yeast Schizosaccharomyces pombe (SpEss1) point to a role of DUF866 protein in mitochondrial oxidative phosphorylation.

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Organizational Affiliation: 
• Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia.
Center for Frontier Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia.
Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia.
Diamond Light Source, Harwell Science and Innovation Campus, Didcot, England, United Kingdom.
Division of Human Biology, School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia.
Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.31 kDa 
• Atom Count: 2,766 
• Modeled Residue Count: 320 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0587 protein C1orf123	A, B	180	Homo sapiens	Mutation(s): 0  Gene Names: C1orf123
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWV4 (Homo sapiens) Explore Q9NWV4  Go to UniProtKB:  Q9NWV4
PHAROS:  Q9NWV4 GTEx:  ENSG00000162384

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	I [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN	H [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	G [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.220 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.32	α = 90
b = 65.35	β = 90
c = 95.05	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
BALBES	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Rahaman, S.N.A., Yusop, J.M., Mohamed-Hussein, Z.A., Wan Mohd, A., Ho, K.L., Teh, A.H., Waterman, J., Ng, C.L.

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Funding Organization	Location	Grant Number
Ministry of Science, Technology and Innovation (Malaysia)	Malaysia	02-01-02-SF0993 (Ministry of Science, Technology and Innovation)

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2021-05-19
  Changes: Database references, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description