[English] 日本語
Yorodumi
- PDB-6fol: Domain II of the human copper chaperone in complex with human Cu,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fol
TitleDomain II of the human copper chaperone in complex with human Cu,Zn superoxide dismutase
Components
  • Copper chaperone for superoxide dismutase
  • Superoxide dismutase [Cu-Zn]
KeywordsMETAL BINDING PROTEIN / heterodimer / copper-chaperone / hSOD1 / protein maturation
Function / homology
Function and homology information


protein maturation by copper ion transfer / superoxide dismutase copper chaperone activity / action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport ...protein maturation by copper ion transfer / superoxide dismutase copper chaperone activity / action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / transmission of nerve impulse / negative regulation of reproductive process / Detoxification of Reactive Oxygen Species / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / protein-disulfide reductase activity / response to axon injury / neuronal action potential / ectopic germ cell programmed cell death / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / glutathione metabolic process / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / locomotory behavior / determination of adult lifespan / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / cellular response to oxidative stress / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / cadherin binding / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Copper chaperone for superoxide dismutase / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSala, F.A. / Wright, G.S.A. / Antonyuk, S.V. / Garratt, R.C. / Hasnain, S.S.
Funding support United Kingdom, Brazil, 5items
OrganizationGrant numberCountry
Motor Neurone Disease AssociationHasnain/Apr15/833-791 United Kingdom
Medical Research Council (United Kingdom)MRF-060-0002-RG-HASNA United Kingdom
Sao Paulo Research Fundation2015/00062-1 Brazil
Sao Paulo Research Fundation2016/24686-7 Brazil
National Council for Scientific and Technological Development407438/2013-0 Brazil
CitationJournal: Plos Biol. / Year: 2019
Title: Molecular recognition and maturation of SOD1 by its evolutionarily destabilised cognate chaperone hCCS.
Authors: Sala, F.A. / Wright, G.S.A. / Antonyuk, S.V. / Garratt, R.C. / Hasnain, S.S.
History
DepositionFeb 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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 / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Copper chaperone for superoxide dismutase
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Copper chaperone for superoxide dismutase
E: Copper chaperone for superoxide dismutase
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,67619
Polymers126,3208
Non-polymers1,35611
Water4,864270
1
A: Copper chaperone for superoxide dismutase
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7114
Polymers31,5802
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-8 kcal/mol
Surface area14080 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4526
Polymers31,5802
Non-polymers8724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-11 kcal/mol
Surface area13970 Å2
MethodPISA
3
E: Copper chaperone for superoxide dismutase
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8035
Polymers31,5802
Non-polymers2233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-10 kcal/mol
Surface area13910 Å2
MethodPISA
4
G: Superoxide dismutase [Cu-Zn]
H: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7114
Polymers31,5802
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-9 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)244.689, 244.689, 182.332
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

-
Protein , 2 types, 8 molecules ADEHBCFG

#1: Protein
Copper chaperone for superoxide dismutase / Superoxide dismutase copper chaperone


Mass: 15816.517 Da / Num. of mol.: 4 / Mutation: Truncation of Domains: I and III
Source method: isolated from a genetically manipulated source
Details: hCCS Domain II with additional residues (GA) from HISTAG
Source: (gene. exp.) Homo sapiens (human) / Gene: CCS / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O14618
#2: Protein
Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 15763.432 Da / Num. of mol.: 4 / Mutation: C57A; C146A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P00441, superoxide dismutase

-
Non-polymers , 4 types, 281 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O9
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% (w/v) PEG 1500 and 0.1 M PCTP buffer pH 7.0 (sodium propionate, sodium cacodylate, and BIS-TRIS propane in the molar ratios 2:1:2, respectively)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.55→49.4 Å / Num. obs: 64704 / % possible obs: 95.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.053 / Rrim(I) all: 0.14 / Net I/σ(I): 9.5
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2 / Num. unique obs: 9558 / CC1/2: 0.409 / Rpim(I) all: 0.335 / Rrim(I) all: 0.877 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DO5, 2C9V

1do5

2c9v


Resolution: 2.55→46.974 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.37 / Details: TLS and NCS were used
RfactorNum. reflection% reflection
Rfree0.2482 3136 4.85 %
Rwork0.208 --
obs0.2099 64691 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→46.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8841 0 64 270 9175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039136
X-RAY DIFFRACTIONf_angle_d0.47412338
X-RAY DIFFRACTIONf_dihedral_angle_d7.9585380
X-RAY DIFFRACTIONf_chiral_restr0.0481327
X-RAY DIFFRACTIONf_plane_restr0.0031699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.58990.39451520.34622826X-RAY DIFFRACTION97
2.5899-2.63240.38291570.34572819X-RAY DIFFRACTION97
2.6324-2.67780.37771400.32812820X-RAY DIFFRACTION97
2.6778-2.72640.33131300.32162829X-RAY DIFFRACTION97
2.7264-2.77890.36931560.3112816X-RAY DIFFRACTION97
2.7789-2.83560.27031510.30012815X-RAY DIFFRACTION97
2.8356-2.89720.31971510.30132815X-RAY DIFFRACTION96
2.8972-2.96460.28981440.28762830X-RAY DIFFRACTION97
2.9646-3.03880.32771410.28172763X-RAY DIFFRACTION95
3.0388-3.12090.29871320.26232798X-RAY DIFFRACTION95
3.1209-3.21270.29511500.24072825X-RAY DIFFRACTION96
3.2127-3.31640.27291310.23152797X-RAY DIFFRACTION96
3.3164-3.43490.26291250.22232806X-RAY DIFFRACTION96
3.4349-3.57240.25791290.21622824X-RAY DIFFRACTION96
3.5724-3.73490.22041680.19922763X-RAY DIFFRACTION95
3.7349-3.93170.22551360.18272772X-RAY DIFFRACTION94
3.9317-4.17790.20461450.16032769X-RAY DIFFRACTION94
4.1779-4.50020.22241180.14362800X-RAY DIFFRACTION94
4.5002-4.95270.19851450.14152787X-RAY DIFFRACTION94
4.9527-5.66830.18981560.15922743X-RAY DIFFRACTION93
5.6683-7.13740.20531530.17292748X-RAY DIFFRACTION93
7.1374-46.98170.18341260.1492790X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.33331.58950.2535.5799-4.78037.6508-0.2703-0.0474-0.26050.2999-0.3581-0.3105-0.0945-0.44880.60140.5162-0.0811-0.2210.38120.0680.6362-61.659216.0268-43.6382
22.4805-0.3119-1.39783.9461.08238.56030.1650.20640.2886-0.20940.12140.5094-0.3054-0.2277-0.3190.4367-0.0605-0.13280.37270.01030.6092-63.849910.3657-45.3397
31.0782-0.10920.57334.9005-0.09391.4996-0.04560.13010.1569-0.1204-0.0427-0.3035-0.09950.00480.0820.4013-0.0918-0.0690.37440.08230.539-55.4632.9619-46.0998
41.66580.4193-1.99053.2237-3.63596.78840.00450.4828-0.0918-0.6818-0.254-0.18250.75680.46590.17430.4979-0.0987-0.11660.37390.10390.7613-44.773423.6306-49.1794
51.3949-0.1121-0.46692.8251-0.16193.80740.1163-0.00910.0747-0.1611-0.03010.4273-0.376-0.1039-0.09910.5439-0.1502-0.070.39310.08210.7404-50.022832.2172-44.7356
67.12141.3562-6.12598.7592-1.24235.58240.1162-0.64251.11710.46870.25111.1602-0.6911.001-0.20740.5509-0.0618-0.12640.52430.01150.8653-50.237939.4462-38.448
72.57190.7872-1.01542.6319-1.57453.8087-0.02980.22640.2153-0.21850.08280.365-0.4504-0.0992-0.04530.5688-0.1137-0.12990.39560.06020.6605-48.572333.9962-46.9561
83.2964-1.0836-1.64731.0781-0.18245.1954-0.2856-0.1850.0790.00450.2966-0.01291.03840.6533-0.11190.576-0.1267-0.10770.36320.07990.5078-57.4786-6.7812-12.7544
92.0696-0.63560.81230.3585-0.72613.39480.1871-0.2773-0.3645-0.1030.17-0.08871.0795-0.8798-0.39630.6614-0.2677-0.17010.43040.09280.7233-64.3078-11.5382-16.0588
101.9443-0.778-2.86295.69391.19624.61780.2432-0.4137-0.63950.17090.09460.15140.0726-0.6968-0.33880.4899-0.1374-0.07070.67840.19390.7107-72.38132.0849-14.4477
115.5374-0.5135-6.34492.6592-0.0287.41890.688-0.31830.26590.0667-0.47722.11090.8736-1.2178-0.23810.6082-0.2702-0.15670.7150.07050.7399-76.755-6.3149-19.0401
124.0822.025-0.88272.4168-1.7434.19020.1814-0.286-0.20040.09010.22170.23150.5935-1.1229-0.38610.5641-0.2212-0.18310.6440.12080.6685-69.1519-8.8278-13.6405
132.7758-0.93453.24982.2046-1.4073.55490.0149-0.8476-0.28620.26250.18680.07060.0492-1.4754-0.19650.5296-0.1904-0.09830.71560.06490.4744-68.0633-2.9611-10.2829
143.70114.11360.99417.65812.89783.58130.8499-0.3129-0.2090.2215-0.0394-0.38830.74330.6005-1.03760.5331-0.1473-0.00620.5386-0.01750.4706-54.318410.2525-11.1258
152.17540.4701-0.06523.6979-1.21813.59070.0298-0.06040.26640.5426-0.00130.0983-0.52120.42480.0590.5417-0.1403-0.09230.4666-0.02390.591-50.294416.3095-13.6896
166.86590.6061-5.08257.1243-1.81194.127-0.3757-0.25470.3629-0.31380.4732-0.23610.80060.5525-0.21040.6489-0.1375-0.05510.40550.01320.7347-47.34-1.5284-15.6166
174.76452.0524-1.56757.2824-2.9537.8082-0.1005-0.41190.4155-0.1846-0.00990.1017-0.03410.54530.1720.4314-0.0605-0.08810.4660.03530.6482-41.826911.4217-25.2624
183.46910.8613-0.35632.774-0.51044.5169-0.0507-0.19890.08880.2767-0.0284-0.2377-0.23650.55130.06970.4985-0.1329-0.13140.4380.02140.6248-44.129113.282-16.7452
194.24091.68042.50592.4758-2.44148.1086-0.136-0.85130.42070.0546-0.06160.8274-0.6955-1.23250.030.33310.0074-0.05280.43680.11350.9091-18.133164.6181-42.8079
205.312-0.1762-1.87812.48251.1442.67980.0047-0.06610.7723-0.32040.10.333-0.13140.4546-0.12080.4132-0.0818-0.04350.38610.18550.7142-22.738561.1815-47.3538
219.8190.19794.99940.9179-0.71893.62240.20171.4323-0.3731-0.43860.34340.7071.03820.5781-0.28450.5679-0.2235-0.19280.44750.15180.5052-27.797152.0627-53.9623
223.38411.8507-0.53213.3773.75377.7303-0.73220.8549-1.3269-0.51110.94970.90071.6345-0.2675-0.0960.6563-0.1184-0.02780.57940.00760.9018-13.365945.3605-49.2978
234.60151.04590.64720.66540.23921.6916-0.0774-0.14750.0259-0.11370.05470.20320.3082-0.21050.02490.4502-0.0832-0.04060.37060.14080.6578-28.78848.8348-41.4695
243.62131.57770.25791.7462-0.23681.6508-0.2030.02350.5253-0.21530.08550.4092-0.0665-0.09930.11680.4346-0.0588-0.06250.37370.12090.6311-27.711352.8794-46.0926
254.5205-0.42560.9055-0.0276-0.87837.4432-0.28880.4938-0.1182-0.8170.3766-0.24910.44570.1726-0.10550.3503-0.0375-0.05640.30690.13680.6377-21.151148.883-49.5817
266.52075.2926-5.33138.501-5.90395.39-0.36410.29160.0856-0.41060.32010.0930.5518-0.67750.1430.451-0.01660.01150.3283-0.07690.5445-2.700450.4135-49.7585
275.4390.9479-4.96513.5741-2.46667.3895-0.1563-0.5442-0.59350.07490.064-0.17291.25860.61860.0920.38050.064-0.05710.34140.05110.65622.397547.3834-39.7589
289.27191.0159-3.49065.0618-1.19662.3267-0.43440.3628-0.4028-0.2859-0.0014-0.77470.18010.39120.50190.3378-0.00370.02050.3411-0.02930.38537.639457.417-52.6584
294.62510.61831.60552.2895-1.83462.3176-0.14640.26580.8981-0.7270.42561.1756-0.4134-1.3399-0.35240.5096-0.0402-0.11610.55120.11240.7479-5.065766.2136-46.1673
309.7169-4.1932-2.04912.8046-0.0886.2191-0.1619-1.28-0.38060.6247-0.1268-0.8539-0.24840.62090.19880.2747-0.01220.05480.5121-0.01680.34498.391565.2908-36.7542
314.36350.7848-1.44672.93020.40973.4658-0.0348-0.1156-0.0095-0.03490.0532-0.09670.21170.2732-0.02640.34260.0234-0.03810.32460.00360.42156.673557.8067-44.2614
329.51170.40880.89133.8273-0.32576.2112-0.01160.22580.653-0.1917-0.05640.7053-0.7073-0.3675-0.17010.3904-0.0620.04210.36150.05220.43949.235470.3032-48.2133
334.62942.7936-1.51443.3521-1.46065.22870.07340.05860.3097-0.58020.03080.6910.70620.0209-0.22850.3726-0.0069-0.06320.37030.02850.5156-5.352153.6882-48.0417
344.7720.3952-3.12674.9972-3.40553.8168-0.0504-0.7746-0.54660.647-0.28190.1525-0.0885-0.56430.20380.5978-0.18680.04960.82980.06050.591-37.195749.9854-14.2007
353.51510.418-3.92353.4173-3.81988.44690.0653-0.14360.00750.24310.08160.77890.1935-0.9536-0.30550.4686-0.2280.05730.8080.03480.8273-42.483851.2087-23.182
368.9321-2.34340.11023.74770.76365.1285-0.86050.8757-1.09990.3160.56320.2165-0.4183-0.46870.24230.689-0.0160.1570.6453-0.01520.6559-38.418560.2597-9.5354
373.89390.84161.93277.85984.48928.79280.06470.09130.61380.0004-0.1304-0.0094-0.753-0.17410.00880.6082-0.05070.09730.6277-0.01690.8549-38.341468.6482-18.081
387.41852.40621.30847.61152.47564.5482-0.0871-0.7051.1331-0.2047-0.7419-0.0846-0.3404-1.15460.75750.5758-0.05020.08820.7545-0.02130.7933-44.090767.3803-21.3929
392.8251-2.4468-2.80692.07821.42248.02770.0548-0.0193-0.2710.40350.15750.4979-0.075-0.5543-0.22890.5064-0.13290.1230.7935-0.00390.8872-42.803657.6634-15.6561
402.6235-4.1625-0.13157.1328-1.28854.161-0.287-0.80120.91320.86090.4709-0.4357-1.4061-0.6622-0.32181.02230.06880.27050.8380.01140.8072-45.261672.8149-10.3605
411.9975-4.4425-1.99379.96676.20088.811-0.5069-0.03430.01520.72930.62850.89320.530.4887-0.00310.6073-0.1650.10870.7180.0280.5736-33.53152.6461-14.0522
429.1003-7.00095.56998.9028-4.92693.4560.2936-0.3651-0.72330.20670.51540.6192-0.04690.2083-0.77610.5657-0.14210.00430.9048-0.06850.6035-20.063153.884-11.3897
431.7753-1.4385-1.37492.6583-1.2767.00640.314-1.1406-0.13760.3349-0.036-0.0912-0.4260.6716-0.28150.5191-0.2462-0.05531.2423-0.03440.6201-12.631152.2787-13.2712
441.5324-0.8813-1.32641.65850.75713.56660.0327-0.9802-0.44970.3495-0.02980.06280.37330.26560.02980.6332-0.1652-0.08691.07170.20360.6589-14.603344.6073-17.7411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 85 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 232 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 22 )
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 75 )
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 85 )
7X-RAY DIFFRACTION7chain 'B' and (resid 86 through 153 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 21 )
9X-RAY DIFFRACTION9chain 'C' and (resid 22 through 47 )
10X-RAY DIFFRACTION10chain 'C' and (resid 48 through 75 )
11X-RAY DIFFRACTION11chain 'C' and (resid 76 through 85 )
12X-RAY DIFFRACTION12chain 'C' and (resid 86 through 132 )
13X-RAY DIFFRACTION13chain 'C' and (resid 133 through 153 )
14X-RAY DIFFRACTION14chain 'D' and (resid 85 through 99 )
15X-RAY DIFFRACTION15chain 'D' and (resid 100 through 132 )
16X-RAY DIFFRACTION16chain 'D' and (resid 133 through 142 )
17X-RAY DIFFRACTION17chain 'D' and (resid 143 through 162 )
18X-RAY DIFFRACTION18chain 'D' and (resid 163 through 232 )
19X-RAY DIFFRACTION19chain 'E' and (resid 83 through 93 )
20X-RAY DIFFRACTION20chain 'E' and (resid 94 through 120 )
21X-RAY DIFFRACTION21chain 'E' and (resid 121 through 132 )
22X-RAY DIFFRACTION22chain 'E' and (resid 133 through 142 )
23X-RAY DIFFRACTION23chain 'E' and (resid 143 through 173 )
24X-RAY DIFFRACTION24chain 'E' and (resid 174 through 216 )
25X-RAY DIFFRACTION25chain 'E' and (resid 217 through 232 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 21 )
27X-RAY DIFFRACTION27chain 'F' and (resid 22 through 36 )
28X-RAY DIFFRACTION28chain 'F' and (resid 37 through 48 )
29X-RAY DIFFRACTION29chain 'F' and (resid 49 through 65 )
30X-RAY DIFFRACTION30chain 'F' and (resid 66 through 75 )
31X-RAY DIFFRACTION31chain 'F' and (resid 76 through 131 )
32X-RAY DIFFRACTION32chain 'F' and (resid 132 through 142 )
33X-RAY DIFFRACTION33chain 'F' and (resid 143 through 153 )
34X-RAY DIFFRACTION34chain 'G' and (resid 1 through 22 )
35X-RAY DIFFRACTION35chain 'G' and (resid 23 through 36 )
36X-RAY DIFFRACTION36chain 'G' and (resid 37 through 56 )
37X-RAY DIFFRACTION37chain 'G' and (resid 57 through 75 )
38X-RAY DIFFRACTION38chain 'G' and (resid 76 through 85 )
39X-RAY DIFFRACTION39chain 'G' and (resid 86 through 125 )
40X-RAY DIFFRACTION40chain 'G' and (resid 126 through 142 )
41X-RAY DIFFRACTION41chain 'G' and (resid 143 through 153 )
42X-RAY DIFFRACTION42chain 'H' and (resid 85 through 99 )
43X-RAY DIFFRACTION43chain 'H' and (resid 100 through 132 )
44X-RAY DIFFRACTION44chain 'H' and (resid 133 through 232 )

+
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://pdbjlvh1.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