[English] 日本語
Yorodumi
- PDB-2gwf: Structure of a USP8-NRDP1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gwf
TitleStructure of a USP8-NRDP1 complex
Components
  • RING finger protein 41
  • Ubiquitin carboxyl-terminal hydrolase 8
KeywordsHYDROLASE/LIGASE / PROTEIN-PROTEIN COMPLEX / E3 LIGASE / PROTEIN UBIQUITINATION / HYDROLASE / PROTEASE / UBL CONJUGATION PATHWAY / Structural Genomics / Structural Genomics Consortium / SGC / HYDROLASE-LIGASE COMPLEX
Function / homology
Function and homology information


regulation of lymphocyte differentiation / interleukin-3 receptor binding / erythropoietin receptor binding / regulation of myeloid cell differentiation / endoplasmic reticulum tubular network / negative regulation of lysosomal protein catabolic process / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome organization / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / protein K48-linked deubiquitination ...regulation of lymphocyte differentiation / interleukin-3 receptor binding / erythropoietin receptor binding / regulation of myeloid cell differentiation / endoplasmic reticulum tubular network / negative regulation of lysosomal protein catabolic process / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome organization / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / protein K48-linked deubiquitination / negative regulation of mitophagy / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / regulation of reactive oxygen species metabolic process / K63-linked deubiquitinase activity / positive regulation of amyloid fibril formation / mitotic cytokinesis / regulation of MAPK cascade / protein deubiquitination / proteasomal protein catabolic process / protein autoubiquitination / extrinsic apoptotic signaling pathway / Regulation of FZD by ubiquitination / cellular response to dexamethasone stimulus / Downregulation of ERBB2:ERBB3 signaling / negative regulation of cell migration / cellular response to nerve growth factor stimulus / Negative regulation of MET activity / regulation of protein stability / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / small GTPase binding / SH3 domain binding / autophagy / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / positive regulation of reactive oxygen species metabolic process / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / regulation of protein localization / midbody / ubiquitinyl hydrolase 1 / dendritic spine / cysteine-type deubiquitinase activity / Ras protein signal transduction / early endosome / postsynaptic density / endosome membrane / Ub-specific processing proteases / protein ubiquitination / cadherin binding / protein domain specific binding / negative regulation of cell population proliferation / cysteine-type endopeptidase activity / perinuclear region of cytoplasm / glutamatergic synapse / proteolysis / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase NRDP1 / NRDP1, C-terminal / USP8 interacting / : / USP8 WW domain / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / USP8 dimerisation domain / USP8 dimerisation domain / Zinc finger, C3HC4 type (RING finger) ...E3 ubiquitin-protein ligase NRDP1 / NRDP1, C-terminal / USP8 interacting / : / USP8 WW domain / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / USP8 dimerisation domain / USP8 dimerisation domain / Zinc finger, C3HC4 type (RING finger) / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / : / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Papain-like cysteine peptidase superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 8 / E3 ubiquitin-protein ligase NRDP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Amino-terminal Dimerization, NRDP1-Rhodanese Interaction, and Inhibited Catalytic Domain Conformation of the Ubiquitin-specific Protease 8 (USP8).
Authors: Avvakumov, G.V. / Walker, J.R. / Xue, S. / Finerty Jr., P.J. / Mackenzie, F. / Newman, E.M. / Dhe-Paganon, S.
History
DepositionMay 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 8
B: RING finger protein 41
C: Ubiquitin carboxyl-terminal hydrolase 8
D: RING finger protein 41
E: Ubiquitin carboxyl-terminal hydrolase 8
F: RING finger protein 41


Theoretical massNumber of molelcules
Total (without water)98,2936
Polymers98,2936
Non-polymers00
Water3,927218
1
A: Ubiquitin carboxyl-terminal hydrolase 8
B: RING finger protein 41


Theoretical massNumber of molelcules
Total (without water)32,7642
Polymers32,7642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ubiquitin carboxyl-terminal hydrolase 8
D: RING finger protein 41


Theoretical massNumber of molelcules
Total (without water)32,7642
Polymers32,7642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ubiquitin carboxyl-terminal hydrolase 8
F: RING finger protein 41


Theoretical massNumber of molelcules
Total (without water)32,7642
Polymers32,7642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.111, 67.094, 99.275
Angle α, β, γ (deg.)90.00, 91.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 8 / Ubiquitin thioesterase 8 / Ubiquitin-specific processing protease 8 / Deubiquitinating enzyme 8 / hUBPy


Mass: 17783.152 Da / Num. of mol.: 3 / Fragment: Rhodanase domain, residues 181-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP8, KIAA0055, UBPY / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P40818, EC: 3.1.2.15
#2: Protein RING finger protein 41


Mass: 14981.053 Da / Num. of mol.: 3 / Fragment: USP8 interaction domain, residues 193-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF41 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9H4P4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG5000 MME, 0.1 M bis-Tris, 1 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 41906 / Num. obs: 41906 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.069 / Net I/σ(I): 21.98
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.15 / Num. unique all: 4352 / Rsym value: 0.46 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU B: 12.467 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23704 2093 5 %RANDOM
Rwork0.2061 ---
obs0.20767 39572 93.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.84 Å2
Baniso -1Baniso -2Baniso -3
1-2.7 Å20 Å2-1.11 Å2
2---1.62 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6170 0 0 218 6388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226298
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9528551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5935770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88824.599287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.209151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1591539
X-RAY DIFFRACTIONr_chiral_restr0.0690.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024716
X-RAY DIFFRACTIONr_nbd_refined0.1680.22771
X-RAY DIFFRACTIONr_nbtor_refined0.2880.24305
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2330
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.214
X-RAY DIFFRACTIONr_mcbond_it0.74634009
X-RAY DIFFRACTIONr_mcangle_it1.20146259
X-RAY DIFFRACTIONr_scbond_it1.43952703
X-RAY DIFFRACTIONr_scangle_it2.23472292
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 162 -
Rwork0.223 2995 -
obs--96.6 %
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)
15.50637.5327-2.221227.7615-1.64084.7076-0.0823-0.09930.36450.37690.38141.2147-0.8022-0.9559-0.29910.01880.1225-0.03430.18550.0110.0898-24.172125.571285.7964
210.695-4.0748-0.82411.85281.272337.236-0.30130.48130.4555-0.38780.5970.6386-2.5944-0.6849-0.29570.29750.0282-0.1272-0.0359-0.0280.0616-20.302333.745791.0782
35.69940.4929-1.30063.8428-1.11356.6829-0.00360.1454-0.2063-0.2345-0.043-0.27150.04680.39940.04670.0820.01270.00030.0907-0.00480.0915-8.016819.463685.0331
41.497-2.04452.71484.4786-0.530110.91130.23160.1983-0.20810.22090.3798-0.05851.08880.7166-0.61150.1522-0.0133-0.07170.00460.050.1448-7.70938.968196.1571
55.7455-1.0771-0.05353.63360.04995.8751-0.0567-0.27440.03380.13380.0343-0.08740.03710.13820.02230.1290.0086-0.00110.07340.00720.0752-3.632419.455397.8278
61.55241.45810.52952.2475-0.50412.31990.06060.0066-0.2007-0.1192-0.04440.19050.1061-0.449-0.01630.08880.0117-0.00980.0867-0.02820.1175-18.058715.101890.1308
71.8485-0.3577-0.19113.773-0.57975.3329-0.041-0.2364-0.13310.51920.12360.2685-0.1777-0.3667-0.08260.08270.02810.04080.08160.01710.1133-17.769315.566596.9625
811.43362.29424.21647.0341-1.561711.7638-0.25470.75580.1033-0.48250.0315-0.1258-0.3920.04670.22320.13880.0706-0.05160.0636-0.00770.0335-15.651425.463176.4458
916.4027-8.77563.907110.1598-3.24645.55880.12590.66010.3041-0.1107-0.6975-1.29290.19310.8340.5716-0.0448-0.02270.03940.10720.10510.20426.857217.473891.7105
104.74953.0982-3.697615.6673-8.0678.0162-0.07630.29650.0427-0.2830.42450.46530.0466-0.2674-0.34820.09650.0002-0.00110.1175-0.00150.10146.769920.352594.1176
1111.39011.74741.4993.1710.52073.452-0.00940.2144-0.5705-0.0450.0547-0.16870.40680.347-0.04540.10640.03520.01940.01270.05350.135118.27957.24795.9897
126.49350.0894-2.23126.1131-0.78476.108-0.0442-0.324-0.24960.7010.0047-0.16060.19980.23920.03940.0876-0.0093-0.05940.10570.03240.070412.887217.4169104.5819
134.89170.28062.25886.7873-0.37883.9911-0.0335-0.11150.47380.0799-0.0497-0.0606-0.5492-0.16180.08310.16060.0085-0.03840.0129-0.03930.09098.730130.688199.4902
143.51981.19680.648412.19874.16153.4212-0.18690.2841-0.2561-0.44180.0959-0.33580.00330.40590.091-0.02540.01190.00530.13010.04240.140519.435719.666790.9954
154.0315-0.4676-0.25823.8315-0.59372.71380.083-0.25560.11870.17360.0859-0.5394-0.11280.6842-0.16890.0484-0.02320.01650.14980.01730.123121.079822.957297.5178
165.3015-0.0221.68453.16121.54464.040.06640.00480.13730.099-0.1524-0.17790.05410.35560.0860.10290.01220.02720.10610.04570.165315.718821.288695.2842
174.17141.2801-3.186315.02358.01267.95830.08450.2659-0.6561-0.17240.17050.21460.89330.0821-0.2550.1238-0.0017-0.0280.1022-0.07290.0943-18.3284-6.500251.5905
180.8176-1.66234.79463.8091-8.134534.18980.24330.5955-0.69030.23190.5150.97652.0767-1.0594-0.75840.2017-0.20710.06990.162-0.14490.1829-27.6421-7.105656.8156
194.1394-0.321-1.018510.27-6.24411.3386-0.11640.240.4571-0.1860.098-0.24-0.4216-0.35120.01840.06280.01020.01230.141-0.06920.0766-22.051211.770851.7725
204.22390.48931.57787.17324.57515.46240.01880.0847-0.0078-0.4786-0.0668-0.0268-0.3068-0.17520.0480.0820.02360.00370.1858-0.01030.085-22.918110.825253.2301
216.4772-1.5958-0.09564.11562.0823.6022-0.1010.08980.14150.15520.2971-0.1112-0.0470.1133-0.19610.02670.00270.01090.1315-0.05510.0801-21.003414.936264.5465
222.7230.7851-0.29672.64610.87994.0359-0.01310.2106-0.10560.09270.305-0.34660.20630.1871-0.2920.00910.0437-0.00580.1238-0.09210.1466-14.03135.134258.6821
232.44330.7881.59972.5212.97689.4155-0.0213-0.0541-0.08750.24220.2562-0.39280.14880.4336-0.23490.03330.0273-0.00410.0616-0.07310.1227-15.68442.674259.928
2418.8934-1.4371.756317.83769.96899.3668-0.12450.3429-0.4438-0.0508-0.15990.4069-0.3835-0.23350.28440.0445-0.0380.00610.1289-0.04910.002-25.19680.121442.9523
25254.9915-53.9648-92.363111.804924.25391.1037-4.89490.41696.12360.70063.5977-0.18920.7036-1.85791.29720.1901-0.1143-0.1985-0.29270.10520.5168-37.662850.587468.0926
264.87051.63832.520219.71424.86248.4371-0.24280.21130.8878-1.3416-0.17990.9685-1.0156-0.20720.4227-0.00980.0882-0.00620.11260.09920.1579-38.984539.112557.2254
2720.34283.23557.82544.80930.76374.3077-0.02770.5058-0.3045-0.17890.2217-0.0828-0.07510.0428-0.19410.07620.01420.01650.1445-0.01060.0899-30.954121.93661.2067
286.3411-4.4745-0.81686.55813.51612.6463-0.09070.32220.9567-0.10950.0926-0.5568-0.31340.2702-0.0018-0.0388-0.0443-0.01370.06830.11170.2603-25.168938.480460.9964
297.50614.00121.957211.5883-4.59916.19850.2221-0.30580.54460.5876-0.06810.0282-0.3302-0.0289-0.1540.04380.03970.02580.1037-0.07460.1139-29.669930.26371.0007
3011.6929-1.41933.05324.30021.21983.157-0.0106-0.1518-0.52740.16490.02270.05710.1692-0.1641-0.0120.02910.00870.05370.14110.0270.0691-38.63618.552568.8791
313.4496-0.3669-0.4433.19790.15862.10740.14850.21950.4582-0.0504-0.14540.1095-0.2336-0.2353-0.00310.02730.0605-0.04180.14260.01690.148-39.051531.924161.1703
325.29750.2322-0.79043.25840.25971.7261-0.0394-0.02460.39240.0473-0.00270.0676-0.2682-0.25450.04210.01740.0461-0.05090.1770.03090.1675-36.836929.345863.3376
3313.8540.0833-3.25532.79813.64775.57210.2980.05380.9292-0.0884-0.04321.0074-0.5594-0.6735-0.25480.2620.19220.14920.06410.05520.0799-9.548449.782779.6678
3422.072622.488510.577223.963915.362325.06320.4930.04940.58690.13650.49861.890.8873-1.2871-0.99160.06250.3242-0.02460.41250.0850.1466-16.048341.431775.9995
354.5082-0.8569-1.61823.9861-0.77786.60570.0765-0.0407-0.09390.12660.0088-0.1956-0.08220.2398-0.08520.10020.00490.01730.0873-0.01150.12062.442938.052478.0364
361.03820.4245-1.2043.3110.35973.5134-0.03840.1538-0.0993-0.2269-0.02010.0181-0.3863-0.07060.05850.10140.02380.01140.09540.01280.05062.977638.882168.2249
370.31552.68151.195122.793910.15844.5272-0.1209-0.36460.6216-0.05350.6311-0.7121-1.54080.8284-0.51020.3855-0.09750.18110.0956-0.01330.01797.182253.942877.8143
383.66392.263.22213.2313-1.010412.66660.26160.35020.4209-0.51110.2052-0.4179-0.98590.1078-0.46680.24050.00670.11420.01540.02540.07345.738248.939168.7669
393.737-1.99291.11496.6211-1.26210.04150.48290.60770.313-0.9273-0.09170.1267-0.99950.2045-0.39120.1620.04670.0754-0.03770.06710.0158-0.05547.691167.8073
403.5509-1.3305-0.33813.08-1.0717.8877-0.2284-0.4284-0.78990.29890.2472-0.3432-0.329-0.4043-0.01890.10340.08560.12340.03420.03140.1046-5.976840.60289.0471
4120.825-13.1713-13.139112.32038.445417.9031-0.50460.2682-1.33910.1468-0.01340.3651.03040.41210.5180.04570.01040.01090.0734-0.00340.130720.76845.982770.7194
4211.80674.36-3.84047.4552-6.08834.98040.08740.0550.41020.22240.06440.1645-0.2849-0.1756-0.15180.0866-0.01030.04610.1065-0.04450.07418.857423.650669.7814
431.73890.1418-0.33817.84511.5241.3317-0.1252-0.00590.022-0.02910.2164-0.1582-0.02180.3274-0.0912-0.0295-0.00270.03440.2029-0.03320.127825.001218.931867.524
449.11410.0742-0.09434.7437-3.75526.4451-0.00750.66750.0375-0.1638-0.039-0.25780.02880.29730.04660.05520.01080.05520.1518-0.0290.110113.798719.667859.272
456.83193.7578-0.400110.1846-4.12598.44780.04390.15220.0946-0.32070.00660.40370.1567-0.5012-0.0505-0.0085-0.0059-0.0110.1286-0.05590.1079-0.026318.904963.6165
4612.15860.90494.22816.9047-2.03716.85340.2325-0.4946-0.1650.3993-0.05590.06650.0169-0.5033-0.17660.0320.01720.09070.10710.01260.096710.315911.229671.5598
473.8965-0.62991.20541.58310.97375.6170.05910.252-0.5094-0.1680.11240.04070.34080.0942-0.17150.07310.01450.0570.11850.02460.183211.968810.485266.4164
485.5577-1.6752-0.0913.72510.76793.690.05120.0897-0.29850.1410.04110.02750.1058-0.1559-0.09230.0485-0.02390.02110.17890.01920.209312.126215.977769.887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA180 - 19219 - 31
2X-RAY DIFFRACTION2AA193 - 19932 - 38
3X-RAY DIFFRACTION3AA200 - 22339 - 62
4X-RAY DIFFRACTION4AA224 - 23363 - 72
5X-RAY DIFFRACTION5AA234 - 24973 - 88
6X-RAY DIFFRACTION6AA250 - 27489 - 113
7X-RAY DIFFRACTION7AA275 - 301114 - 140
8X-RAY DIFFRACTION8AA302 - 315141 - 154
9X-RAY DIFFRACTION9BB197 - 21114 - 28
10X-RAY DIFFRACTION10BB212 - 22229 - 39
11X-RAY DIFFRACTION11BB223 - 24440 - 61
12X-RAY DIFFRACTION12BB245 - 26062 - 77
13X-RAY DIFFRACTION13BB261 - 27478 - 91
14X-RAY DIFFRACTION14BB275 - 28292 - 99
15X-RAY DIFFRACTION15BB283 - 298100 - 115
16X-RAY DIFFRACTION16BB299 - 317116 - 134
17X-RAY DIFFRACTION17CC180 - 19019 - 29
18X-RAY DIFFRACTION18CC191 - 19930 - 38
19X-RAY DIFFRACTION19CC200 - 21139 - 50
20X-RAY DIFFRACTION20CC212 - 22651 - 65
21X-RAY DIFFRACTION21CC227 - 24766 - 86
22X-RAY DIFFRACTION22CC248 - 28287 - 121
23X-RAY DIFFRACTION23CC283 - 304122 - 143
24X-RAY DIFFRACTION24CC305 - 313144 - 152
25X-RAY DIFFRACTION25DD192 - 1989 - 15
26X-RAY DIFFRACTION26DD199 - 21116 - 28
27X-RAY DIFFRACTION27DD212 - 22229 - 39
28X-RAY DIFFRACTION28DD223 - 24440 - 61
29X-RAY DIFFRACTION29DD245 - 25762 - 74
30X-RAY DIFFRACTION30DD258 - 27175 - 88
31X-RAY DIFFRACTION31DD272 - 29589 - 112
32X-RAY DIFFRACTION32DD296 - 317113 - 134
33X-RAY DIFFRACTION33EE180 - 19019 - 29
34X-RAY DIFFRACTION34EE191 - 19630 - 35
35X-RAY DIFFRACTION35EE197 - 22636 - 65
36X-RAY DIFFRACTION36EE227 - 26166 - 100
37X-RAY DIFFRACTION37EE262 - 272101 - 111
38X-RAY DIFFRACTION38EE273 - 282112 - 121
39X-RAY DIFFRACTION39EE283 - 301122 - 140
40X-RAY DIFFRACTION40EE302 - 316141 - 155
41X-RAY DIFFRACTION41FF196 - 21013 - 27
42X-RAY DIFFRACTION42FF211 - 22328 - 40
43X-RAY DIFFRACTION43FF224 - 24441 - 61
44X-RAY DIFFRACTION44FF245 - 25862 - 75
45X-RAY DIFFRACTION45FF259 - 27276 - 89
46X-RAY DIFFRACTION46FF273 - 28090 - 97
47X-RAY DIFFRACTION47FF281 - 30098 - 117
48X-RAY DIFFRACTION48FF301 - 317118 - 134

+
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