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- PDB-4a4c: Structure of phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex -

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Basic information

Entry
Database: PDB / ID: 4a4c
TitleStructure of phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex
Components
  • E3 UBIQUITIN-PROTEIN LIGASE CBL
  • TYROSINE-PROTEIN KINASE ZAP-70
  • UBIQUITIN-CONJUGATING ENZYME E2 D2
KeywordsLIGASE/TRANSFERASE / LIGASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / T cell migration / regulation of Rap protein signal transduction / entry of bacterium into host cell / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / (E3-independent) E2 ubiquitin-conjugating enzyme / flotillin complex ...T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / T cell migration / regulation of Rap protein signal transduction / entry of bacterium into host cell / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / (E3-independent) E2 ubiquitin-conjugating enzyme / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / beta selection / positive thymic T cell selection / positive regulation of alpha-beta T cell differentiation / positive regulation of T cell differentiation / positive regulation of epidermal growth factor receptor signaling pathway / T cell receptor complex / E2 ubiquitin-conjugating enzyme / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to testosterone / B cell activation / cellular response to platelet-derived growth factor stimulus / negative regulation of epidermal growth factor receptor signaling pathway / Translocation of ZAP-70 to Immunological synapse / TGF-beta receptor signaling activates SMADs / response to starvation / protein monoubiquitination / ubiquitin conjugating enzyme activity / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / protein autoubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / positive regulation of calcium-mediated signaling / ubiquitin ligase complex / extrinsic component of cytoplasmic side of plasma membrane / FLT3 signaling by CBL mutants / cell surface receptor protein tyrosine kinase signaling pathway / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / T cell activation / ephrin receptor binding / phosphotyrosine residue binding / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / cellular response to nerve growth factor stimulus / response to activity / Negative regulators of DDX58/IFIH1 signaling / Regulation of signaling by CBL / calcium-mediated signaling / Negative regulation of FGFR3 signaling / response to gamma radiation / Peroxisomal protein import / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / EGFR downregulation / Negative regulation of FGFR1 signaling / non-specific protein-tyrosine kinase / Spry regulation of FGF signaling / non-membrane spanning protein tyrosine kinase activity / Constitutive Signaling by EGFRvIII / RING-type E3 ubiquitin transferase / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Negative regulation of MET activity / Inactivation of CSF3 (G-CSF) signaling / receptor tyrosine kinase binding / CLEC7A (Dectin-1) signaling / cytokine-mediated signaling pathway / cilium / FCERI mediated NF-kB activation / positive regulation of receptor-mediated endocytosis / SH3 domain binding / peptidyl-tyrosine phosphorylation / protein polyubiquitination / ubiquitin-protein transferase activity / Signaling by CSF1 (M-CSF) in myeloid cells / male gonad development / ubiquitin protein ligase activity / cell-cell junction / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / E3 ubiquitin ligases ubiquitinate target proteins / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / Neddylation / T cell receptor signaling pathway / growth cone / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / protein tyrosine kinase activity / response to ethanol
Similarity search - Function
Prokaryotic RING finger family 4 / Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain ...Prokaryotic RING finger family 4 / Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Adaptor protein Cbl, N-terminal domain superfamily / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / Transcription Elongation Factor S-II; Chain A / UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / SH2 domain / SHC Adaptor Protein / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / EF-hand domain pair / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Zinc finger, RING/FYVE/PHD-type / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL / Tyrosine-protein kinase ZAP-70 / Ubiquitin-conjugating enzyme E2 D2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å
AuthorsDou, H. / Buetow, L. / Hock, A. / Sibbet, G.J. / Vousden, K.H. / Huang, D.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural Basis for Autoinhibition and Phosphorylation-Dependent Activation of C-Cbl
Authors: Dou, H. / Buetow, L. / Hock, A. / Sibbet, G.J. / Vousden, K.H. / Huang, D.T.
History
DepositionOct 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Other
Revision 1.2Apr 3, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE CBL
B: TYROSINE-PROTEIN KINASE ZAP-70
C: UBIQUITIN-CONJUGATING ENZYME E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4236
Polymers63,2523
Non-polymers1713
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-13.8 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.285, 75.285, 459.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE CBL / CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE / PROTO-ONCOGENE C-CBL / RING FINGER PROTEIN 55 / SIGNAL ...CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE / PROTO-ONCOGENE C-CBL / RING FINGER PROTEIN 55 / SIGNAL TRANSDUCTION PROTEIN CBL / C-CBL


Mass: 45152.805 Da / Num. of mol.: 1
Fragment: TKB DOMAIN, LINKER HELIX REGION, AND RING DOMAIN, RESIDUES 47-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Protein UBIQUITIN-CONJUGATING ENZYME E2 D2 / UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2 / UBIQUITIN-CONJUGATING ...UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2 / UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2 / UBIQUITIN-PROTEIN LIGASE D2 / UBCH5B


Mass: 16755.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: P62837, ubiquitin-protein ligase

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Protein/peptide , 1 types, 1 molecules B

#2: Protein/peptide TYROSINE-PROTEIN KINASE ZAP-70 / 70 KDA ZETA-ASSOCIATED PROTEIN / SYK-RELATED TYROSINE KINASE / ZAP-70


Mass: 1344.275 Da / Num. of mol.: 1 / Fragment: ZAP-70 PEPTIDE, RESIDUES 286-297 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
References: UniProt: P43403, non-specific protein-tyrosine kinase

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Non-polymers , 3 types, 13 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL GS RESULTED FROM CLONING AND TEV CLEAVAGE. Y371 IS PHOSPHORYLATED. CORRESPONDS TO 286- ...N-TERMINAL GS RESULTED FROM CLONING AND TEV CLEAVAGE. Y371 IS PHOSPHORYLATED. CORRESPONDS TO 286-297 IN HUMAN ZAP-70 SEQUENCE. Y7 IS PHOSPHORYLATED.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growTemperature: 277 K
Details: 50 MM HEPES, PH 7.5, 0.2 M KCL AND 31-35% (V/V) PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH) AT 4 DEGREES CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 22290 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 16.8 % / Biso Wilson estimate: 84.14 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 4.2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2ESK, 1FBV
Resolution: 2.704→29.325 Å / SU ML: 0.79 / σ(F): 1.35 / Phase error: 26.88 / Stereochemistry target values: ML
Details: CHAIN A RESIDUE 47, CHAIN B, 1-3, CHAIN C RESIDUE 1 AND 129 ARE DISORDERED. FOLLOWING RESIDUES ARE BUILT AS ALA BECAUSE SIDE CHAIN DENSITY IS NOT VISIBLE. CHAIN A RESIDUES ...Details: CHAIN A RESIDUE 47, CHAIN B, 1-3, CHAIN C RESIDUE 1 AND 129 ARE DISORDERED. FOLLOWING RESIDUES ARE BUILT AS ALA BECAUSE SIDE CHAIN DENSITY IS NOT VISIBLE. CHAIN A RESIDUES 58,61,65,105,107,135,137, 191,192,322,354,358,359,361,362,364,365,366,367,369,379 AND CHAIN C RESIDUES 128,131,132,134,136,139,143.
RfactorNum. reflection% reflection
Rfree0.2677 1134 5.1 %
Rwork0.2027 --
obs0.2059 22290 99.31 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.117 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso mean: 101 Å2
Baniso -1Baniso -2Baniso -3
1--2.7785 Å20 Å20 Å2
2---2.7785 Å20 Å2
3---5.5569 Å2
Refinement stepCycle: LAST / Resolution: 2.704→29.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4261 0 3 10 4274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094378
X-RAY DIFFRACTIONf_angle_d1.3085955
X-RAY DIFFRACTIONf_dihedral_angle_d16.3771592
X-RAY DIFFRACTIONf_chiral_restr0.091649
X-RAY DIFFRACTIONf_plane_restr0.006766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7041-2.8270.44811260.35142520X-RAY DIFFRACTION98
2.827-2.97590.35411540.28672570X-RAY DIFFRACTION100
2.9759-3.16220.33231440.27482583X-RAY DIFFRACTION100
3.1622-3.4060.35541430.23982580X-RAY DIFFRACTION100
3.406-3.74820.32071480.24452630X-RAY DIFFRACTION100
3.7482-4.28910.2151400.18512649X-RAY DIFFRACTION100
4.2891-5.39830.22781390.16772747X-RAY DIFFRACTION100
5.3983-29.32620.23791400.17712877X-RAY DIFFRACTION98
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)
11.0446-1.5207-0.21892.2193-0.33923.1048-0.13590.0105-0.57210.2268-0.39590.0199-0.03090.5050.53261.0079-0.16580.19850.54990.13541.1654-14.193122.4472-23.0256
23.2253-0.47481.37133.74380.37193.16560.30210.34970.4672-0.5834-0.1679-0.6846-0.590.4991-0.03740.90.02830.30710.54910.32710.8349-18.344115.3644-27.3176
38.12983.83221.30348.0688-4.48934.39710.98891.0676-1.0295-1.6172-0.1296-0.5458-0.0506-0.4689-0.35561.61070.54490.13930.82340.00320.4166-30.56322.4031-42.0857
43.3817-1.7359-0.84862.8493-0.254.76080.69820.5484-0.0112-0.7202-0.65650.0101-0.5686-0.6485-0.09070.81820.2502-0.02620.46270.09590.5763-39.063313.1966-28.6578
53.25462.5555-0.34643.59460.65497.19170.4209-0.1457-0.42440.4743-0.47510.23310.4636-0.81340.05710.68240.09930.0310.55140.10530.5824-46.064111.0427-17.0002
61.68931.00811.51350.76341.44293.24281.0538-0.1365-1.7313-3.34680.27941.881.5746-0.6978-1.13071.4274-0.0823-0.11330.78010.09171.0955-42.8433-16.7048-27.2496
74.8301-1.2429-0.15387.4365-4.53232.93940.02450.0592-0.6627-0.46570.42211.08410.9727-0.9457-0.25941.0465-0.1286-0.07290.40630.15220.8956-36.501-15.5881-16.1546
85.0175-2.2939-3.26637.0588-3.16925.65480.61780.1926-1.2295-0.803-0.13740.97410.467-0.4665-0.25530.7858-0.0571-0.12090.27510.25970.8465-33.8891-12.0024-19.6816
95.85827.0457-5.19989.5047-5.91284.70650.2462-0.4283-0.67631.8470.0065-0.21690.1366-0.3289-0.41580.9702-0.00530.16090.60960.17690.6891-38.42769.0766-9.9939
108.6925-1.53933.83625.4761-2.03488.7770.70020.3728-0.9841-0.1619-0.06080.16562.0270.0907-0.43741.1954-0.00220.02630.30760.14721.0805-27.2612-29.4465-2.5658
110.545-1.3720.00165.3052.00432.16120.22221.0476-0.041-0.46940.3878-0.8595-0.05250.248-0.10191.03231.24730.46161.2347-0.01252.4698-3.9081-30.1944-1.6684
121.1091.17150.38821.26890.48983.77170.1803-0.3447-0.7411-0.3336-0.0287-0.53610.69830.3709-0.20860.89170.15860.10630.36470.16541.0013-18.6312-20.62544.0334
133.7728-2.93541.67963.95371.43275.1341-0.047-0.35380.0462-1.29440.2196-0.8292-0.30340.6797-0.00031.12160.16520.43380.08770.34421.0982-20.5867-14.4836-6.0138
143.6524.78692.19956.93460.75028.250.88930.7083-0.50870.2432-0.44540.66330.75241.0041-0.53441.09030.3970.1970.59720.01171.004-14.6846-23.6707-5.7654
154.8359-3.403-4.9149.02130.4036.3999-0.94241.6893-0.4799-0.31810.5707-1.3548-0.48040.21460.6950.79640.11990.0291.51320.11141.598-1.5758-13.94932.1623
160.8323-1.4224-0.88862.44661.73586.50670.66530.4462-0.17380.37380.6927-0.48952.02551.8147-0.85921.26010.8119-0.08650.95770.21921.5418-0.5048-27.61237.8251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 47:83)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 84:183)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 184:212)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 213:295)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 296:347)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 348:373)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 374:410)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 411:435)
9X-RAY DIFFRACTION9CHAIN B
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 2:38)
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 39:48)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 49:84)
13X-RAY DIFFRACTION13CHAIN C AND (RESSEQ 85:98)
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 99:111)
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 112:130)
16X-RAY DIFFRACTION16CHAIN C AND (RESSEQ 131:147)

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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

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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

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