[English] 日本語
Yorodumi
- PDB-6i5n: Crystal structure of SOCS2:Elongin C:Elongin B in complex with gr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i5n
TitleCrystal structure of SOCS2:Elongin C:Elongin B in complex with growth hormone receptor peptide
Components
  • Elongin-B
  • Elongin-C
  • Growth hormone receptor peptide
  • Suppressor of cytokine signaling 2
KeywordsSIGNALING PROTEIN / Complex
Function / homology
Function and homology information


JAK pathway signal transduction adaptor activity / negative regulation of receptor signaling pathway via JAK-STAT / 1-phosphatidylinositol-3-kinase regulator activity / target-directed miRNA degradation / elongin complex / VCB complex / phosphatidylinositol 3-kinase complex / growth hormone receptor binding / Cul5-RING ubiquitin ligase complex / growth hormone receptor signaling pathway ...JAK pathway signal transduction adaptor activity / negative regulation of receptor signaling pathway via JAK-STAT / 1-phosphatidylinositol-3-kinase regulator activity / target-directed miRNA degradation / elongin complex / VCB complex / phosphatidylinositol 3-kinase complex / growth hormone receptor binding / Cul5-RING ubiquitin ligase complex / growth hormone receptor signaling pathway / Cul2-RING ubiquitin ligase complex / negative regulation of multicellular organism growth / cell surface receptor signaling pathway via JAK-STAT / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / phosphatidylinositol phosphate biosynthetic process / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / mammary gland alveolus development / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Growth hormone receptor signaling / cellular response to hormone stimulus / RNA Polymerase II Pre-transcription Events / Negative regulation of FLT3 / lactation / positive regulation of neuron differentiation / Interleukin-7 signaling / transcription corepressor binding / transcription elongation by RNA polymerase II / regulation of cell growth / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Vif-mediated degradation of APOBEC3G / insulin-like growth factor receptor binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / response to estradiol / protein-macromolecule adaptor activity / Neddylation / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / protein ubiquitination / intracellular signal transduction / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
SOCS box / Suppressor of cytokine signalling 2 / SOCS2, SH2 domain / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin C; Chain C, domain 1 ...SOCS box / Suppressor of cytokine signalling 2 / SOCS2, SH2 domain / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin C; Chain C, domain 1 / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Suppressor of cytokine signaling 2 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsKung, W.W. / Ramachandran, S. / Makukhin, N. / Bruno, E. / Ciulli, A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
European Research CouncilERC-2012-StG-311460 DrugE3CRLs United Kingdom
Wellcome Trust100476/Z/12/Z United Kingdom
Wellcome Trust094090/Z/10/Z United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase.
Authors: Kung, W.W. / Ramachandran, S. / Makukhin, N. / Bruno, E. / Ciulli, A.
History
DepositionNov 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / pdbx_seq_map_depositor_info / struct
Item: _audit_author.identifier_ORCID / _audit_author.name ..._audit_author.identifier_ORCID / _audit_author.name / _pdbx_seq_map_depositor_info.one_letter_code / _struct.title
Revision 1.2Jun 19, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Suppressor of cytokine signaling 2
B: Elongin-B
C: Elongin-C
D: Suppressor of cytokine signaling 2
E: Elongin-B
F: Elongin-C
J: Growth hormone receptor peptide
K: Growth hormone receptor peptide
I: Growth hormone receptor peptide
L: Growth hormone receptor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,97313
Polymers89,76010
Non-polymers2143
Water9,224512
1
A: Suppressor of cytokine signaling 2
B: Elongin-B
C: Elongin-C
K: Growth hormone receptor peptide
I: Growth hormone receptor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9396
Polymers44,8805
Non-polymers591
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Suppressor of cytokine signaling 2
E: Elongin-B
F: Elongin-C
J: Growth hormone receptor peptide
L: Growth hormone receptor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0357
Polymers44,8805
Non-polymers1552
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.177, 156.763, 57.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-248-

HOH

21E-266-

HOH

31E-306-

HOH

-
Components

-
Protein , 3 types, 6 molecules ADBECF

#1: Protein Suppressor of cytokine signaling 2 / SOCS-2 / Cytokine-inducible SH2 protein 2 / CIS-2 / STAT-induced STAT inhibitor 2 / SSI-2


Mass: 19411.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOCS2, CIS2, SSI2, STATI2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14508
#2: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11852.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370
#3: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10974.616 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369

-
Protein/peptide , 1 types, 4 molecules JKIL

#4: Protein/peptide
Growth hormone receptor peptide


Mass: 1320.407 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 3 types, 515 molecules

#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: Sodium cacodylate, cobalt chloride, MES, ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→113.55 Å / Num. obs: 73251 / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 17.1
Reflection shellResolution: 1.98→2.01 Å

-
Processing

Software
NameVersionClassification
PHENIX(dev_2420: ???)refinement
Cootmodel building
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→54.042 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 22.68
RfactorNum. reflection% reflection
Rfree0.2264 3750 2.72 %
Rwork0.1899 --
obs0.1909 72170 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→54.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5910 0 7 512 6429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016048
X-RAY DIFFRACTIONf_angle_d1.0648201
X-RAY DIFFRACTIONf_dihedral_angle_d17.6463629
X-RAY DIFFRACTIONf_chiral_restr0.067945
X-RAY DIFFRACTIONf_plane_restr0.0061026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00510.31141420.27664906X-RAY DIFFRACTION100
2.0051-2.03140.26421350.26714957X-RAY DIFFRACTION100
2.0314-2.05930.26191420.2495023X-RAY DIFFRACTION100
2.0593-2.08870.27611380.23224932X-RAY DIFFRACTION100
2.0887-2.11990.23641340.23144955X-RAY DIFFRACTION100
2.1199-2.1530.22291340.22044981X-RAY DIFFRACTION100
2.153-2.18830.24121420.21534921X-RAY DIFFRACTION100
2.1883-2.2260.25121400.21445034X-RAY DIFFRACTION100
2.226-2.26650.24551340.2194926X-RAY DIFFRACTION100
2.2665-2.31010.2271420.19874997X-RAY DIFFRACTION100
2.3101-2.35730.25791400.19644928X-RAY DIFFRACTION100
2.3573-2.40850.23521380.19654994X-RAY DIFFRACTION100
2.4085-2.46450.30421380.19914914X-RAY DIFFRACTION100
2.4645-2.52620.2641380.19625006X-RAY DIFFRACTION100
2.5262-2.59450.29711410.19714961X-RAY DIFFRACTION100
2.5945-2.67080.27031410.20024884X-RAY DIFFRACTION100
2.6708-2.7570.28871410.21335063X-RAY DIFFRACTION100
2.757-2.85560.30971380.20634912X-RAY DIFFRACTION100
2.8556-2.96990.25151350.20014957X-RAY DIFFRACTION100
2.9699-3.1050.22371400.20384989X-RAY DIFFRACTION100
3.105-3.26870.26041430.19584958X-RAY DIFFRACTION100
3.2687-3.47350.18971410.17664953X-RAY DIFFRACTION100
3.4735-3.74160.22351370.16994979X-RAY DIFFRACTION100
3.7416-4.1180.18731410.1494991X-RAY DIFFRACTION100
4.118-4.71360.14591390.13234943X-RAY DIFFRACTION100
4.7136-5.93750.1571390.17064963X-RAY DIFFRACTION100
5.9375-54.0620.20211370.19314960X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.51190.4658-0.51261.9898-2.12847.41790.1574-0.05460.04350.12050.13480.3245-0.0015-0.2282-0.2770.1167-0.0417-0.01630.24440.01020.2385-16.065931.0492-26.5836
21.71560.28-0.12388.81890.81795.8127-0.09281.12790.2075-0.8070.1396-0.6741-0.2660.7288-0.00260.2529-0.0180.02010.61660.09350.2357-4.002237.3208-43.2955
34.83071.0659-1.26952.27550.78443.6177-0.12060.2547-0.4494-0.0789-0.1401-0.32930.1620.43770.2670.1004-0.01510.01030.26340.03560.2294-3.499131.6673-31.4966
44.50450.4166-0.24350.04230.05270.0895-0.0669-0.13790.34510.18760.1542-0.09430.2343-0.0251-0.10.20810.0267-0.0130.27610.02040.31380.397634.7824-18.3074
53.014-0.26021.13322.5285-4.7329.5801-0.24350.08350.05410.4311-0.0831-0.296-0.4120.1610.35910.1733-0.0216-0.00770.2303-0.01060.2148-8.849240.9339-22.4256
65.5897-0.98711.09460.4173-0.04540.9304-0.1040.27550.46160.0386-0.1167-0.2577-0.24020.29020.16120.2329-0.0542-0.01230.270.11980.2861-6.867844.3232-33.6788
73.3488-0.4483-0.54211.97472.56796.660.005-0.2690.0506-0.0211-0.0201-0.1157-0.41260.18020.0090.1884-0.0096-0.02130.19820.04040.1381-26.51248.702-26.4882
83.4693-2.305-4.74384.34031.46898.5085-0.17-0.7844-0.75110.3336-0.01180.07190.3010.11430.12490.1632-0.0194-0.03450.24930.05580.1984-25.972243.0007-23.4673
97.0338-4.11163.54667.6102-3.22773.76590.10050.4442-0.3291-0.1745-0.24510.1337-0.19750.45540.07570.2481-0.0528-0.01830.26130.00380.1123-30.471150.122-55.849
104.0244-1.3456-1.98373.0407-0.30016.5766-0.12870.10340.01350.0146-0.04340.0705-0.26030.35120.19280.1962-0.0601-0.04880.16-0.01670.1062-32.683649.6328-57.5305
118.25920.2416-4.15882.1678-2.65247.3422-0.03040.4292-0.1767-0.57420.11470.25260.1172-0.1851-0.07720.2693-0.0401-0.05320.1977-0.01660.1394-36.792447.9838-65.4533
128.80131.74110.95328.31810.17256.16850.0090.64760.3897-0.46530.06030.2654-0.3032-0.4571-0.05180.28150.0179-0.01450.21140.04590.1364-40.768754.6801-66.2184
137.7125-1.71630.29055.50372.28015.1925-0.00550.22170.6844-0.1650.0264-0.2539-1.3950.6922-0.03930.4933-0.1823-0.02580.35410.04850.2352-27.587758.3392-64.9622
140.50241.0631-1.08234.1188-1.30994.0555-0.11380.24160.12350.2413-0.1942-0.3049-0.51860.94630.35960.2829-0.0811-0.01610.2827-0.00050.1416-27.354353.0807-55.0638
158.5274-3.27474.27185.1057-4.2454.04290.11731.49450.7408-1.26640.26470.9287-0.4658-1.9174-0.29720.68590.1632-0.05810.70910.13330.4631-47.767961.0311-69.0353
160.75160.113-0.00471.8667-3.34816.61520.03670.02810.24490.16170.19060.3988-1.5701-0.9951-0.21310.59490.0502-0.02180.18650.03430.308-40.63461.4143-52.6687
174.6702-0.1851-0.43480.4869-0.62190.8903-0.6801-1.58820.8620.86840.7806-0.87470.25910.7735-1.06481.6502-0.3851-0.3251.2036-0.40430.433-30.098760.1502-27.6413
183.4184-0.1549-0.32354.7544-2.03355.6265-0.02860.0573-0.0904-0.31680.01120.05380.2404-0.17460.03720.1138-0.0131-0.01580.1232-0.03590.149-40.272641.8278-46.8065
194.99943.95061.11153.2861.10230.7352-0.08550.01310.26550.2682-0.23331.30750.2857-0.32680.34330.4403-0.04390.08240.3446-0.14410.4714-52.059131.6199-47.7787
206.3132-0.7053-0.55282.56130.36554.12660.05950.1657-0.18730.0412-0.1275-0.00490.00870.11740.05650.1481-0.0139-0.0140.130.02330.0851-30.400344.918-43.0994
214.04973.84621.40053.86821.97326.3135-0.1116-0.2004-0.0647-0.09010.0922-0.0985-0.3525-0.27090.08150.16710.02260.00750.18590.00240.1787-33.552847.3452-33.2031
224.67184.8871-3.966.0163-4.61993.56-0.02290.06190.0217-0.17260.14590.3070.0918-0.4126-0.12580.1351-0.0134-0.04240.24310.03230.2876-20.930121.9262-81.4713
231.5468-1.1762-0.10911.99030.8421.52110.1851-0.8265-0.31910.3876-0.3214-0.58330.10790.74560.15340.2546-0.0717-0.08960.51120.20450.424-12.903314.5362-64.6757
242.6421-1.21042.00954.7937-0.28112.6876-0.1759-0.15-0.6938-0.3299-0.1853-0.89730.32890.43530.16430.21610.0570.06530.31580.14570.4954-13.24249.7906-76.1165
250.96250.67661.87091.28382.42135.1118-0.3010.1053-0.9191-0.184-0.4976-0.52231.10190.73080.57710.57350.06950.1120.43410.27860.8604-16.6589-0.364-70.4772
263.2831-0.46260.8061.35390.2966.79440.04290.1498-0.0576-0.0829-0.1502-0.0533-0.21470.10990.11590.1997-0.06310.02430.14180.02110.1558-35.344112.9615-75.1813
275.79771.4488-1.6064.6455-0.31223.67770.04930.1953-0.1390.1698-0.103-0.2641-0.12010.54080.09920.2394-0.07740.00580.16060.03510.0945-42.259710.9436-46.4135
281.48420.12670.42231.5677-0.72053.55140.0744-0.0460.19770.1343-0.15990.004-0.33190.50590.10110.2424-0.09250.01640.1961-0.03920.1353-43.660412.633-44.7558
293.38920.1322.08212.1555-2.03323.37180.0743-0.43470.4650.78360.09090.0115-1.15040.20850.08120.4069-0.1268-0.00430.1943-0.07470.1628-46.901815.6758-36.9012
308.2824-3.63670.00624.58372.36634.7095-0.0534-0.36230.02120.5570.07660.2562-0.2911-0.01650.04720.3109-0.06880.0610.148-0.0120.1807-53.344411.2764-36.113
312.43173.9962.35537.06634.39922.8762-0.0218-0.0088-0.12260.324-0.0382-0.17340.09270.2749-0.05360.2815-0.0709-0.00120.2437-0.01410.1859-45.34461.5929-37.5828
326.9793-1.35282.74782.46621.33422.6695-0.17370.3371-0.0053-0.107-0.2398-0.27310.33770.6230.31310.2754-0.02540.01160.3037-0.00710.2344-36.01094.4575-40.9055
332.47161.3633-1.0091.4454-0.04463.1044-0.171-0.10950.0705-0.02090.08210.00050.11760.29150.11720.2777-0.0521-0.02740.15650.02660.1363-42.81637.9993-48.1519
342.1571-2.6628-0.14065.56592.1093.80991.0532-1.65321.3421.5498-0.54961.2348-0.6208-1.5197-0.29520.5688-0.07050.09510.5428-0.11640.394-62.70388.3271-32.7592
354.18450.9544-5.35820.2744-1.55268.6282-0.22270.2794-0.2379-0.28440.18320.23390.7109-0.68370.1120.3364-0.09-0.01610.1682-0.01520.2242-56.11195.0088-49.6587
360.9133-0.9208-1.08670.95251.40065.0930.01120.9663-0.6339-0.7471-0.3303-0.0490.4686-0.0839-0.2561.2606-0.18490.31680.7185-0.34340.4201-48.52991.5778-73.3486
373.39991.077-0.51132.91640.79382.15430.1844-0.00830.2765-0.0854-0.11140.0028-0.4728-0.0447-0.03160.3632-0.05140.03060.1358-0.00690.2012-47.715723.2106-55.6912
382.40522.77731.27495.63442.16971.2086-0.1764-0.04840.5843-0.18790.03470.6033-0.10340.08520.15060.32530.0089-0.01890.2649-0.01110.3233-50.39129.7435-59.3375
394.33-0.8252-0.06882.126-0.68413.96480.0862-0.12650.07970.0736-0.1819-0.2244-0.13690.27260.09160.2618-0.09340.00040.14830.0310.1471-38.545214.516-62.1263
402.31660.6764-0.00494.59560.41071.9953-0.010.86650.1212-0.25720.2025-0.8148-0.15250.6196-0.18010.1447-0.03590.00220.4060.02320.38855.153435.3674-31.9827
412.1378-1.19180.59092.8227-1.56362.08360.4503-0.4667-0.69940.4959-0.0816-1.03040.68130.3844-0.3430.38240.0637-0.11380.61590.22810.815-4.79175.3651-69.4654
425.7433-0.4152-1.27531.83650.01182.5732-0.06750.0611.46650.18020.152-0.5896-0.50360.15570.02350.2942-0.0956-0.10130.3240.07470.66271.652347.922-24.968
430.36010.70160.37091.54350.65270.85210.3940.0873-0.5792-0.72850.2727-0.33720.2412-0.013-0.05660.66530.1257-0.06520.51560.21711.3765-13.5171-3.4018-75.7823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 100 )
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 115 )
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 131 )
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 162 )
7X-RAY DIFFRACTION7chain 'A' and (resid 163 through 184 )
8X-RAY DIFFRACTION8chain 'A' and (resid 185 through 198 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 9 )
10X-RAY DIFFRACTION10chain 'B' and (resid 10 through 23 )
11X-RAY DIFFRACTION11chain 'B' and (resid 24 through 35 )
12X-RAY DIFFRACTION12chain 'B' and (resid 36 through 45 )
13X-RAY DIFFRACTION13chain 'B' and (resid 46 through 60 )
14X-RAY DIFFRACTION14chain 'B' and (resid 61 through 79 )
15X-RAY DIFFRACTION15chain 'B' and (resid 80 through 84 )
16X-RAY DIFFRACTION16chain 'B' and (resid 85 through 95 )
17X-RAY DIFFRACTION17chain 'B' and (resid 96 through 103 )
18X-RAY DIFFRACTION18chain 'C' and (resid 16 through 46 )
19X-RAY DIFFRACTION19chain 'C' and (resid 47 through 58 )
20X-RAY DIFFRACTION20chain 'C' and (resid 59 through 96 )
21X-RAY DIFFRACTION21chain 'C' and (resid 97 through 112 )
22X-RAY DIFFRACTION22chain 'D' and (resid 30 through 46 )
23X-RAY DIFFRACTION23chain 'D' and (resid 47 through 81 )
24X-RAY DIFFRACTION24chain 'D' and (resid 82 through 131 )
25X-RAY DIFFRACTION25chain 'D' and (resid 132 through 154 )
26X-RAY DIFFRACTION26chain 'D' and (resid 155 through 198 )
27X-RAY DIFFRACTION27chain 'E' and (resid 1 through 9 )
28X-RAY DIFFRACTION28chain 'E' and (resid 10 through 23 )
29X-RAY DIFFRACTION29chain 'E' and (resid 24 through 35 )
30X-RAY DIFFRACTION30chain 'E' and (resid 36 through 45 )
31X-RAY DIFFRACTION31chain 'E' and (resid 46 through 55 )
32X-RAY DIFFRACTION32chain 'E' and (resid 56 through 65 )
33X-RAY DIFFRACTION33chain 'E' and (resid 66 through 79 )
34X-RAY DIFFRACTION34chain 'E' and (resid 80 through 84 )
35X-RAY DIFFRACTION35chain 'E' and (resid 85 through 95 )
36X-RAY DIFFRACTION36chain 'E' and (resid 96 through 101 )
37X-RAY DIFFRACTION37chain 'F' and (resid 16 through 47 )
38X-RAY DIFFRACTION38chain 'F' and (resid 48 through 66 )
39X-RAY DIFFRACTION39chain 'F' and (resid 67 through 112 )
40X-RAY DIFFRACTION40chain 'I' and (resid -4 through 5 )
41X-RAY DIFFRACTION41chain 'J' and (resid -4 through 5 )
42X-RAY DIFFRACTION42chain 'K' and (resid -3 through 5 )
43X-RAY DIFFRACTION43chain 'L' and (resid -2 through 5 )

+
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