Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.26 kDa 
• Atom Count: 858 
• Modelled Residue Count: 104 
• Deposited Residue Count: 104 
• Unique protein chains: 1

2N9I

Solution structure of reduced human cytochrome c

• PDB DOI: 10.2210/pdb2N9I/pdb
• BMRB: 25907

• Classification: ELECTRON TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-24 Released: 2016-02-17 
• Deposition Author(s): Imai, M., Saio, T., Kumeta, H., Uchida, T., Inagaki, F., Ishimori, K.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c

Imai, M., Saio, T., Kumeta, H., Uchida, T., Inagaki, F., Ishimori, K.

(2016) Biochem Biophys Res Commun 469: 978-984

• PubMed: 26718409 
• DOI: 10.1016/j.bbrc.2015.12.079
• Primary Citation of Related Structures:  
  2N9I, 2N9J


• PubMed Abstract: 
  

Redox-dependent changes in the structure and dynamics of human cytochrome c (Cyt c) were investigated by solution NMR. We found significant structural changes in several regions, including residues 23-28 (loop 3), which were further corroborated by chemical shift differences between the reduced and oxidized states of Cyt c. These differences are essential for discriminating redox states in Cyt c by cytochrome c oxidase (CcO) during electron transfer reactions. Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments identified that the region around His33 undergoes conformational exchanges on the μs-ms timescale, indicating significant redox-dependent structural changes. Because His33 is not part of the interaction site for CcO, our data suggest that the dynamic properties of the region, which is far from the interaction site for CcO, contribute to conformational changes during electron transfer to CcO.

---

Organizational Affiliation: 

Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	A	104	Homo sapiens	Mutation(s): 0  Gene Names: CYCS, CYC
UniProt & NIH Common Fund Data Resources
Find proteins for P99999 (Homo sapiens) Explore P99999  Go to UniProtKB:  P99999
PHAROS:  P99999

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	B [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 
• OLDERADO: 2N9I Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-11-24 
• Released Date: 2016-02-17 
Deposition Author(s): Imai, M., Saio, T., Kumeta, H., Uchida, T., Inagaki, F., Ishimori, K.

Revision History  

• Version 1.0: 2016-02-17
  Type: Initial release