[English] 日本語
Yorodumi
- PDB-9v6c: Neutron crystal structure of the oxidized form of b5R at pD 7.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9v6c
TitleNeutron crystal structure of the oxidized form of b5R at pD 7.5
ComponentsNADH-cytochrome b5 reductase 3
KeywordsOXIDOREDUCTASE / fatty acid synthesis / methemoglobin reduction / xenobiotic oxidation / antioxidant defense
Function / homology
Function and homology information


cytochrome-b5 reductase / cytochrome-b5 reductase activity, acting on NAD(P)H / cholesterol biosynthetic process / FAD binding / flavin adenine dinucleotide binding / mitochondrial outer membrane / endoplasmic reticulum membrane / mitochondrion
Similarity search - Function
NADH:cytochrome b5 reductase-like / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADH-cytochrome b5 reductase 3
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHirano, Y. / Kurihara, K. / Kusaka, K. / Ostermann, A. / Hikita, M. / Kimura, S. / Miki, K. / Tamada, T.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR17G7 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)Photon and Quantum Basic Research Coordinated Development Program Japan
Japan Society for the Promotion of Science (JSPS)JP20K06523 Japan
Japan Society for the Promotion of Science (JSPS)JP17K07325 Japan
Japan Society for the Promotion of Science (JSPS)JP2544037 Japan
CitationJournal: Structure / Year: 2025
Title: Structural basis of hydride and proton transfer reactions revealed by the detection of hydrogen atoms in mammalian NADH-cytochrome b 5 reductase.
Authors: Hirano, Y. / Kurihara, K. / Kusaka, K. / Ostermann, A. / Hikita, M. / Kimura, S. / Miki, K. / Tamada, T.
History
DepositionMay 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADH-cytochrome b5 reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0276
Polymers30,8731
Non-polymers1,1545
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-7 kcal/mol
Surface area13880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.558, 72.100, 84.769
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein NADH-cytochrome b5 reductase 3 / B5R / Cytochrome b5 reductase / Diaphorase-1


Mass: 30872.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CYB5R3, DIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P83686, cytochrome-b5 reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 12% PEG 3350, 10mM potassium phosphate pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 2.66 Å
DetectorType: BIODIFF / Detector: IMAGE PLATE / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.66 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 54529 / % possible obs: 88.3 % / Redundancy: 2.6 % / Biso Wilson estimate: 8.05 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.091 / Net I/σ(I): 6.6
Reflection shellResolution: 1.45→1.48 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2804 / CC1/2: 0.7 / Rpim(I) all: 0.328

-
Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→19.59 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.91
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Neutron data
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 2424 5.12 %Select the same reflections as PDB code 5GV8
Rwork0.1773 44931 --
obs0.1787 47335 88.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0256000
NEUTRON DIFFRACTIONf_angle_d1.95910217
NEUTRON DIFFRACTIONf_chiral_restr0.092384
NEUTRON DIFFRACTIONf_plane_restr0.014911
NEUTRON DIFFRACTIONf_dihedral_angle_d16.9931547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.28141290.22272374NEUTRON DIFFRACTION80
1.48-1.510.22021480.20382500NEUTRON DIFFRACTION86
1.51-1.550.2191200.1992593NEUTRON DIFFRACTION88
1.55-1.590.26021300.1922602NEUTRON DIFFRACTION88
1.59-1.630.20221420.18022616NEUTRON DIFFRACTION88
1.63-1.680.23421380.17092610NEUTRON DIFFRACTION89
1.68-1.730.20371620.16592584NEUTRON DIFFRACTION88
1.73-1.790.23981210.16672578NEUTRON DIFFRACTION87
1.79-1.860.21321420.16792513NEUTRON DIFFRACTION85
1.86-1.950.1921430.16392500NEUTRON DIFFRACTION84
1.95-2.050.18221290.162565NEUTRON DIFFRACTION86
2.05-2.180.17291230.16112639NEUTRON DIFFRACTION88
2.18-2.350.19561450.16652585NEUTRON DIFFRACTION87
2.35-2.580.18341610.1622759NEUTRON DIFFRACTION92
2.58-2.960.1911650.1692831NEUTRON DIFFRACTION95
2.96-3.720.17411620.17162988NEUTRON DIFFRACTION98
3.72-19.590.22471640.21213074NEUTRON DIFFRACTION96

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more