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- PDB-7w3o: Crystal structure of human CYB5R3 -

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Basic information

Entry
Database: PDB / ID: 7w3o
TitleCrystal structure of human CYB5R3
ComponentsNADH-cytochrome b5 reductase 3 soluble form
KeywordsOXIDOREDUCTASE / ER-phagy / Ufmylation / Ufm1 / Reductase
Function / homology
Function and homology information


nitric-oxide synthase complex / cytochrome-b5 reductase / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase activity, acting on NAD(P)H / Phase I - Functionalization of compounds / blood circulation / AMP binding / cholesterol biosynthetic process / hemoglobin complex / nitric oxide biosynthetic process ...nitric-oxide synthase complex / cytochrome-b5 reductase / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase activity, acting on NAD(P)H / Phase I - Functionalization of compounds / blood circulation / AMP binding / cholesterol biosynthetic process / hemoglobin complex / nitric oxide biosynthetic process / FAD binding / lipid droplet / mitochondrial membrane / ADP binding / NAD binding / azurophil granule lumen / mitochondrial outer membrane / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / extracellular region / membrane / cytosol / cytoplasm
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsNoda, N.N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H05707 Japan
Japan Science and TechnologyJPMJCR20E3 Japan
CitationJournal: Nat Commun / Year: 2022
Title: The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3.
Authors: Ishimura, R. / El-Gowily, A.H. / Noshiro, D. / Komatsu-Hirota, S. / Ono, Y. / Shindo, M. / Hatta, T. / Abe, M. / Uemura, T. / Lee-Okada, H.C. / Mohamed, T.M. / Yokomizo, T. / Ueno, T. / ...Authors: Ishimura, R. / El-Gowily, A.H. / Noshiro, D. / Komatsu-Hirota, S. / Ono, Y. / Shindo, M. / Hatta, T. / Abe, M. / Uemura, T. / Lee-Okada, H.C. / Mohamed, T.M. / Yokomizo, T. / Ueno, T. / Sakimura, K. / Natsume, T. / Sorimachi, H. / Inada, T. / Waguri, S. / Noda, N.N. / Komatsu, M.
History
DepositionNov 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH-cytochrome b5 reductase 3 soluble form
B: NADH-cytochrome b5 reductase 3 soluble form
C: NADH-cytochrome b5 reductase 3 soluble form
D: NADH-cytochrome b5 reductase 3 soluble form
E: NADH-cytochrome b5 reductase 3 soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,0659
Polymers157,9235
Non-polymers3,1424
Water3,459192
1
A: NADH-cytochrome b5 reductase 3 soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3702
Polymers31,5851
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-8 kcal/mol
Surface area13830 Å2
MethodPISA
2
B: NADH-cytochrome b5 reductase 3 soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3702
Polymers31,5851
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-8 kcal/mol
Surface area13770 Å2
MethodPISA
3
C: NADH-cytochrome b5 reductase 3 soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3702
Polymers31,5851
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-8 kcal/mol
Surface area13650 Å2
MethodPISA
4
D: NADH-cytochrome b5 reductase 3 soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3702
Polymers31,5851
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-8 kcal/mol
Surface area13570 Å2
MethodPISA
5
E: NADH-cytochrome b5 reductase 3 soluble form


Theoretical massNumber of molelcules
Total (without water)31,5851
Polymers31,5851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.360, 79.920, 169.400
Angle α, β, γ (deg.)90.000, 98.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
NADH-cytochrome b5 reductase 3 soluble form


Mass: 31584.504 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYB5R3, DIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00387
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 1500, 10% 2-propanol, 0.1M bicine at pH 8.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→49.5694 Å / Num. obs: 78626 / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.259 / Net I/σ(I): 12.5
Reflection shellResolution: 2.46→2.61 Å / Rmerge(I) obs: 1.78 / Num. unique obs: 2536

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5H

3w5h


Resolution: 2.46→49.5694 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 4016 5.11 %
Rwork0.2312 74610 -
obs0.2327 78626 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.41 Å2 / Biso mean: 69.3488 Å2 / Biso min: 17.69 Å2
Refinement stepCycle: final / Resolution: 2.46→49.5694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10761 0 292 192 11245
Biso mean--65.02 56.85 -
Num. residues----1350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.46-2.4890.35681380.311925362674
2.489-2.51930.31151450.298525392684
2.5193-2.55120.31021390.297325372676
2.5512-2.58480.35911450.30825912736
2.5848-2.62020.36071250.322525192644
2.6202-2.65760.36931620.320825652727
2.6576-2.69730.32891260.295325662692
2.6973-2.73940.31411340.276225972731
2.7394-2.78430.27581680.257724962664
2.7843-2.83230.30291410.24325722713
2.8323-2.88380.25791390.232925312670
2.8838-2.93930.30151280.242325902718
2.9393-2.99930.26961120.235525912703
2.9993-3.06450.30541440.25325582702
3.0645-3.13580.28061380.256825862724
3.1358-3.21420.28441400.262325312671
3.2142-3.30110.27411460.245225442690
3.3011-3.39820.28471560.237425602716
3.3982-3.50780.30551370.239425862723
3.5078-3.63320.24661360.219825932729
3.6332-3.77860.2381290.205825682697
3.7786-3.95050.24731260.215226042730
3.9505-4.15870.25561380.203325722710
4.1587-4.41910.20541230.193625932716
4.4191-4.760.19361330.193825942727
4.76-5.23860.20711370.204125742711
5.2386-5.99550.24121500.215526142764
5.9955-7.54940.23611500.235826102760
7.5494-49.56940.27281310.239526932824
Refinement TLS params.Method: refined / Origin x: 38.2108 Å / Origin y: 11.5161 Å / Origin z: 11.5491 Å
111213212223313233
T0.2605 Å2-0.0007 Å20.0118 Å2-0.1813 Å20.014 Å2--0.2306 Å2
L0.2726 °20.0711 °20.0396 °2--0.0613 °2-0.0025 °2--0.0124 °2
S0.0372 Å °-0.0658 Å °-0.0579 Å °-0.0237 Å °0.0304 Å °0.0257 Å °0.0062 Å °0.0171 Å °0.0531 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 275
2X-RAY DIFFRACTION1allA1301
3X-RAY DIFFRACTION1allB4 - 275
4X-RAY DIFFRACTION1allB1301
5X-RAY DIFFRACTION1allC4 - 275
6X-RAY DIFFRACTION1allC1301
7X-RAY DIFFRACTION1allD6 - 275
8X-RAY DIFFRACTION1allD1301
9X-RAY DIFFRACTION1allE5 - 275
10X-RAY DIFFRACTION1allS1 - 192

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