[English] 日本語
Yorodumi
- PDB-7q42: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q42
TitleCrystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B
Components
  • Bromodomain adjacent to zinc finger domain protein 2B
  • E3 ubiquitin-protein ligase HERC2
KeywordsPROTEIN BINDING / 7-bladed beta-propeller E3 ubiquitin-protein ligase HERC2 RCC1-like Domain2 RLD2 BAZ2B chromatin reader DXDKDED motif
Function / homology
Function and homology information


SUMO binding / HECT-type E3 ubiquitin transferase / negative regulation of Notch signaling pathway / SUMOylation of DNA damage response and repair proteins / centriole / guanyl-nucleotide exchange factor activity / Nonhomologous End-Joining (NHEJ) / intracellular protein transport / G2/M DNA damage checkpoint / neuron differentiation ...SUMO binding / HECT-type E3 ubiquitin transferase / negative regulation of Notch signaling pathway / SUMOylation of DNA damage response and repair proteins / centriole / guanyl-nucleotide exchange factor activity / Nonhomologous End-Joining (NHEJ) / intracellular protein transport / G2/M DNA damage checkpoint / neuron differentiation / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin remodeling / DNA repair / ubiquitin protein ligase binding / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
HERC2, APC10 domain / HERC2, zinc finger, ZZ-type / Beta-propeller repeat TECPR / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / CPH domain / Mouse development and cellular proliferation protein Cullin-7 ...HERC2, APC10 domain / HERC2, zinc finger, ZZ-type / Beta-propeller repeat TECPR / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / : / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / BAZ2A/BAZ2B, bromodomain / Zinc finger ZZ-type signature. / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Galactose-binding-like domain superfamily / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Ribosomal protein L2, domain 2 / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
CITRIC ACID / E3 ubiquitin-protein ligase HERC2 / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95002486823 Å
AuthorsDemenge, A. / Howard, E. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / McEwen, A.G. / Trave, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of chromatin reader BAZ2B
Authors: Demenge, A. / Howard, E. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / McEwen, A.G. / Trave, G.
History
DepositionOct 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HERC2
C: E3 ubiquitin-protein ligase HERC2
E: E3 ubiquitin-protein ligase HERC2
D: Bromodomain adjacent to zinc finger domain protein 2B
B: Bromodomain adjacent to zinc finger domain protein 2B
F: Bromodomain adjacent to zinc finger domain protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,0779
Polymers133,5006
Non-polymers5763
Water15,331851
1
A: E3 ubiquitin-protein ligase HERC2
B: Bromodomain adjacent to zinc finger domain protein 2B


Theoretical massNumber of molelcules
Total (without water)44,5002
Polymers44,5002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: E3 ubiquitin-protein ligase HERC2
D: Bromodomain adjacent to zinc finger domain protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6923
Polymers44,5002
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: E3 ubiquitin-protein ligase HERC2
F: Bromodomain adjacent to zinc finger domain protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8844
Polymers44,5002
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.980, 107.980, 241.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein E3 ubiquitin-protein ligase HERC2 / HECT domain and RCC1-like domain-containing protein 2 / HECT-type E3 ubiquitin transferase HERC2


Mass: 42770.566 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HERC2 / Production host: Escherichia coli (E. coli)
References: UniProt: O95714, HECT-type E3 ubiquitin transferase
#2: Protein/peptide Bromodomain adjacent to zinc finger domain protein 2B / hWALp4


Mass: 1729.513 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: n-terminally biotinylated peptide via 1,13-diamino-4,7,10-trioxatridecan-succinamic acid
Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UIF8
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: hanging drop 20% PEG 3350 0.18M tris amonium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978564 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978564 Å / Relative weight: 1
ReflectionResolution: 1.95→49.29 Å / Num. obs: 104649 / % possible obs: 99.92 % / Redundancy: 27.0621601735 % / Biso Wilson estimate: 29.4271306625 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.93
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 1.03 / Num. unique obs: 7616 / CC1/2: 0.61

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KCI

3kci


Resolution: 1.95002486823→49.289620536 Å / SU ML: 0.197426353888 / Cross valid method: FREE R-VALUE / σ(F): 1.3364811143 / Phase error: 19.8875984756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206296338153 5167 4.94345687989 %
Rwork0.167870694125 99355 -
obs0.16974605582 104522 99.9168331597 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.9076128539 Å2
Refinement stepCycle: LAST / Resolution: 1.95002486823→49.289620536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8433 0 39 851 9323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01067798198878638
X-RAY DIFFRACTIONf_angle_d1.1341394845911665
X-RAY DIFFRACTIONf_chiral_restr0.08300374245781293
X-RAY DIFFRACTIONf_plane_restr0.00674149692571513
X-RAY DIFFRACTIONf_dihedral_angle_d20.0233136723092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95002486823-1.97220.3145612906381770.2775805060563251X-RAY DIFFRACTION99.0179087233
1.9722-1.99540.3308304104951780.2588239588493254X-RAY DIFFRACTION99.4494349464
1.9954-2.01970.2966771876241520.234906606483247X-RAY DIFFRACTION99.8237885463
2.0197-2.04530.2604915131041430.2242323731583318X-RAY DIFFRACTION99.9711149624
2.0453-2.07220.238884396621770.2085034535613238X-RAY DIFFRACTION99.941469125
2.0722-2.10060.2488663900091670.2060420822673281X-RAY DIFFRACTION99.9710060887
2.1006-2.13060.2243947322031720.2072661624113255X-RAY DIFFRACTION99.9416739574
2.1306-2.16240.2434694383841730.2023852683463274X-RAY DIFFRACTION99.9420121774
2.1624-2.19620.2543064295391690.1996506408883248X-RAY DIFFRACTION99.9707431246
2.1962-2.23220.2190396410391630.1923962275873300X-RAY DIFFRACTION99.9711316397
2.2322-2.27070.2358080685421580.1905148153013251X-RAY DIFFRACTION99.8828010548
2.2707-2.3120.2362657166341530.1891705234783315X-RAY DIFFRACTION100
2.312-2.35640.2165795173932120.1797803290283247X-RAY DIFFRACTION100
2.3564-2.40450.2226626281171600.1800889737963338X-RAY DIFFRACTION100
2.4045-2.45680.2103926836141660.1765466823743263X-RAY DIFFRACTION100
2.4568-2.5140.2253442991531740.1738414238463282X-RAY DIFFRACTION99.9710731848
2.514-2.57680.2087969087351910.1709190718033259X-RAY DIFFRACTION100
2.5768-2.64650.2216726839041790.1759206967623313X-RAY DIFFRACTION99.9713713141
2.6465-2.72440.2325860825371760.1740178268543279X-RAY DIFFRACTION100
2.7244-2.81230.2227262939481840.1750087159833277X-RAY DIFFRACTION100
2.8123-2.91280.2256351730151710.1722151186813328X-RAY DIFFRACTION100
2.9128-3.02940.2098278372391750.1710619770533297X-RAY DIFFRACTION100
3.0294-3.16730.1859831631211490.1650752404493362X-RAY DIFFRACTION100
3.1673-3.33420.181449369921800.1651595679633334X-RAY DIFFRACTION99.9715504979
3.3342-3.54310.2017844245081720.1589431981953342X-RAY DIFFRACTION100
3.5431-3.81650.1725162563581780.141476446823351X-RAY DIFFRACTION100
3.8165-4.20040.1523476394761710.1255823223153370X-RAY DIFFRACTION100
4.2004-4.80780.1644458679371680.1313702875963426X-RAY DIFFRACTION100
4.8078-6.05560.1827244214791730.1528218753753435X-RAY DIFFRACTION100
6.0556-49.2896205360.2361961972132060.1836529028483620X-RAY DIFFRACTION99.7133176961
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)
10.459876582271-0.152557985407-0.0207058417710.2147823837610.1578792737940.352638901550.1247482027010.214048708857-0.0490932971022-0.147252496593-0.2505356439570.03749019256670.0373270829671-0.1616626772145.00329831556E-80.2297674695980.08364058718610.007570369107540.285455833446-0.008031264424590.133393052541-21.2510955594-40.5841427688-49.804185506
20.444975869155-0.45390185925-0.002423559510120.7045538233910.2438768207930.5372570023850.02153581241570.0726633042849-0.0389597243465-0.0452289267268-0.1070809180580.0960380260266-0.0755044996593-0.1553735263015.95517702452E-90.132567634320.0578343747817-0.002636243594690.2301533845020.01014457609640.139174733318-29.3094701278-30.4246466223-38.5030860433
30.382916341482-0.3115615204040.1084715678690.3685970629420.09912147147420.582517143023-0.0118498931061-0.02589280718710.0907007933724-0.0641853407111-0.05131596672770.0714897511073-0.164910574413-0.2046933552627.60054279352E-80.1900013232690.09654233498990.01529054880680.239182104470.00602820603190.205352032107-29.1898812106-22.022506124-31.0460737249
40.787502784822-0.259764134521-0.2123679764120.1703061260230.3499661833680.38801853772-0.0940559583344-0.07258748326690.07613131413750.02824508908180.040647828427-0.0401758765368-0.107243117137-0.08141779131741.49023555661E-80.2378571375420.05788191032490.009885283063550.1695552985490.005984948575730.166985837891-17.4801596943-23.8688647712-23.7149603345
51.01715877454-0.8788546932850.1092479136390.1885907855-0.02757055133440.614935141671-0.0236582765856-0.03825283451590.09168015730430.03369263602420.0212290052949-0.0774906844492-0.0174620372140.120102839225-5.83655001976E-100.1574368599760.008373370289810.006534036950780.1770011572840.02037994666660.146204662753-4.23919775846-32.7578101541-27.5434923637
60.1131059276380.1292975782990.1125738550760.3338092702870.1948818274780.3002822164620.0003336264454930.1656455831750.0525950131410.0323538728772-0.0452223129784-0.08368081821040.07490609507420.1577816666556.59639352919E-80.1537379524040.0542707160320.04650905446180.2689229629590.05771830658840.184108080644-3.7845134721-36.4629083551-42.9118098934
70.3600297067370.542954131876-0.1999580097440.3197432277560.1534372153260.4973074734440.05709641529990.0855794287410.0128973077821-0.0758904699082-0.000252511985289-0.02093215420150.03688699528640.02416335150439.65448306912E-80.217291434220.06686974194590.0370025086950.2388977336430.02669286877830.165393185685-10.3915761731-42.5640133137-45.9151593772
80.4859753572070.450848089480.02343748545490.213675669873-0.2187839760590.20632325209-0.1457754109770.3034016566310.00540692331422-0.1182774306170.04634775046630.02637941799390.235048144677-0.107595968502-9.66368763386E-90.213934899236-0.0189844576669-0.000957209461270.224231613744-0.002951828573820.1495136504-16.6911902314-59.8789631868-10.6551912743
90.3434729150370.204347241221-0.4803374119030.279937561722-0.03911907811410.0735791164277-0.07322037419270.216478378465-0.0976881576325-0.07232625333210.03293315217140.06914496046510.150188933001-0.1391566018399.78343814154E-80.205203712759-0.0444560610256-0.02166215396520.2413098407-0.03716705361490.158507699567-25.8777169408-66.3440641609-4.76025306556
100.5985038776940.502215116786-0.5402149613380.262363922858-0.07711961627870.989723839369-0.01874623557310.1114790321250.0674761600120.00477688566792-0.01790335469690.1069471097440.108581849904-0.1341508829671.23256591485E-80.130663517922-0.035775233687-0.004640980139760.177107084704-0.01917145522580.234992857391-33.3970601146-61.87247847386.17379262525
110.2870089183420.6614744498570.2425898198370.639123087461-0.1465171546480.3202853069950.0851571377579-0.03932745389220.03301703912620.0550054353053-0.1242700490830.1421224373380.0272880502561-0.06026413855449.72836836706E-90.188154198288-0.01610011254170.0391600670290.178109044361-0.02765510769590.200117364465-27.5590467311-54.623077527817.9728886847
120.7933908112160.4580819047360.1183640125380.5138150197960.2032939632120.4991262793840.0955532274841-0.04802012465960.08372661279560.0895743107646-0.0587128338177-0.0150808526562-0.04918170485880.05150983797451.93124490215E-80.193746975343-0.01584854398390.001729167751330.149485000997-0.009370154630510.141455299042-13.0276302664-47.529524647315.1256758357
130.562659285334-0.135885863098-0.5100129640020.2051048792570.08105829878430.6618438510240.07361902867750.04996903182190.04628906996530.0771898961388-0.0734100254431-0.0941510783635-0.1043256326640.0782532926459-4.47056298422E-80.172901617949-0.00424196068849-0.01173696454280.1711754899450.02374080561680.16092253899-7.30109419465-49.0580106827-1.01615471615
140.0853478821380.178247266466-0.1037190849950.0768310449271-0.1256303664590.2338446999140.05943259914640.138640802142-0.007719560276480.02013016205170.03882124331940.082312799813-0.0173147021258-0.08727051546741.46269404325E-70.1831604484090.0276357155624-0.00397977112530.2039581108670.02633201206410.15108850012-15.0433523957-50.5458026869-8.44170748546
150.953661546179-0.259495301289-0.034346909660.2620276923840.03117729588140.5519542955830.1054484215610.3706972097120.230757056583-0.0585787362512-0.096505451217-0.195002082902-0.0194723389190.01212130390842.06088100916E-80.1562799211390.008644086981590.03427376277070.2197397661660.05514606340930.25350442755126.4004098743-49.0835432503-30.248142359
160.602730347034-0.01406169451020.3720297301820.270408654927-0.5221461710590.6179722954730.04861601925380.121744267470.05374153925730.00171603796263-0.0973158782794-0.1721306614160.03697860974910.0423284120667-2.70379496929E-90.1362215810690.00925345461223-0.006405907025810.173224681949-0.01030264256040.33363016818936.3241806484-57.3055252288-19.7009708722
171.187489547810.1217547599360.2796868290620.286145336743-0.6017820088590.8932064347860.0424532750542-0.113288582769-0.0275329889650.0206153660842-0.00498333515977-0.3135564399960.01843417594620.0324636122659-1.98376545147E-80.15564396840.00800175452523-0.07839092727970.153228636910.01309313259770.3491665934335.5596771182-60.876065493-9.48886812786
181.60713224754-0.1707106269310.1831423901030.275677008567-0.3154913181670.5558959351960.0589165237638-0.216034107894-0.1223277415390.02067344205230.00903664949493-0.08158420337960.0423970395516-0.1258470925892.49571849625E-90.150913847844-0.0245603152869-0.0516500718090.1491977521050.03729261020.1495630958416.0934519286-62.5425208828-7.69941507807
190.413439251258-0.1944271544520.3693806599440.455927513114-0.1483457654120.2397622754550.09653947708340.0601292305973-0.00936168322830.0438956876401-0.0599388062520.00700700882045-0.0352849279191-0.15690715041-1.26502083502E-70.1403836037660.00341026432494-0.01181799373060.2172965745180.00223978578710.1687146777798.12654961421-55.1246812466-22.8353853139
200.1354752516850.01120645313130.1899191164470.154690498366-0.120790581480.03479435324540.05820828053040.151124828536-0.05331849939910.00318721554127-0.0044795064402-0.0915233832307-0.0080514994614-0.0548789849627.97651284526E-70.1871187099650.00111490269973-0.007141680596520.250049308613-0.0278280425080.19706837721914.6543113907-56.6014569674-30.984832185
21-0.0079847415655-0.0194762347555-0.005474879759040.0223898179769-0.03612557279770.0118068975441-0.253395041094-0.630321032657-0.130035588792-0.168350896272-0.0720861711496-0.2478464921340.765650989933-0.344143623146-2.04408512642E-70.4578763971980.0549490735429-0.006154671537050.3579441314130.005371309752870.509605655043-7.65215759767-68.41353630384.07521247908
220.0538918372847-0.0728025447881-0.0328304513780.05483848836440.01759577420230.0133915414873-0.27226128799-0.0668986182556-0.2147570548730.412799493509-0.212864112969-0.1667733481850.0115123474726-0.348487774261-4.30952807943E-60.428314914521-0.06548632208540.03459094171260.3965561408550.0366059703640.327714641274-20.3534610258-50.4334736581-32.1321607628
23-0.00046388735776-0.0226709821365-0.008972652131130.02134387607940.0252579490341-0.00105123805176-0.0919969420664-0.179410237030.230708414822-0.1016268843740.155056215810.0501543835722-0.4348490783440.04212225407021.11434026178E-50.550614277209-0.0010582239169-0.006999507376970.400578488549-0.1296400595190.56308945149718.002993711-40.9450814218-15.3024873788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2958 through 3000 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3001 through 3082 )
3X-RAY DIFFRACTION3chain 'A' and (resid 3083 through 3106 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3107 through 3169 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3170 through 3250 )
6X-RAY DIFFRACTION6chain 'A' and (resid 3251 through 3282 )
7X-RAY DIFFRACTION7chain 'A' and (resid 3283 through 3326 )
8X-RAY DIFFRACTION8chain 'C' and (resid 2959 through 3000 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3001 through 3037 )
10X-RAY DIFFRACTION10chain 'C' and (resid 3038 through 3106 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3107 through 3169 )
12X-RAY DIFFRACTION12chain 'C' and (resid 3170 through 3250 )
13X-RAY DIFFRACTION13chain 'C' and (resid 3251 through 3302 )
14X-RAY DIFFRACTION14chain 'C' and (resid 3303 through 3326 )
15X-RAY DIFFRACTION15chain 'E' and (resid 2959 through 3037 )
16X-RAY DIFFRACTION16chain 'E' and (resid 3038 through 3082 )
17X-RAY DIFFRACTION17chain 'E' and (resid 3083 through 3144 )
18X-RAY DIFFRACTION18chain 'E' and (resid 3145 through 3250 )
19X-RAY DIFFRACTION19chain 'E' and (resid 3251 through 3302 )
20X-RAY DIFFRACTION20chain 'E' and (resid 3303 through 3326 )
21X-RAY DIFFRACTION21chain 'D' and (resid 649 through 658 )
22X-RAY DIFFRACTION22chain 'B' and (resid 649 through 658 )
23X-RAY DIFFRACTION23chain 'F' and (resid 650 through 656 )

+
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