[English] 日本語
Yorodumi
- PDB-3op0: Crystal structure of Cbl-c (Cbl-3) TKB domain in complex with EGF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3op0
TitleCrystal structure of Cbl-c (Cbl-3) TKB domain in complex with EGFR pY1069 peptide
Components
  • Epidermal growth factor receptor
  • Signal transduction protein CBL-C
KeywordsSIGNALING PROTEIN/SIGNALING PROTEIN REGULATOR / Structural Genomics / Structural Genomics Consortium / SGC / Signal transduction protein / SH3-binding protein / SIGNALING PROTEIN-SIGNALING PROTEIN REGULATOR complex
Function / homology
Function and homology information


response to glial cell derived neurotrophic factor / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / epidermal growth factor receptor binding / Developmental Lineage of Mammary Gland Myoepithelial Cells / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma ...response to glial cell derived neurotrophic factor / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / epidermal growth factor receptor binding / Developmental Lineage of Mammary Gland Myoepithelial Cells / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / response to UV-A / ubiquitin-dependent endocytosis / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / Signaling by EGFR / ERBB2 Activates PTK6 Signaling / digestive tract morphogenesis / intracellular vesicle / eyelid development in camera-type eye / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / protein insertion into membrane / negative regulation of epidermal growth factor receptor signaling pathway / protein tyrosine kinase activator activity / Respiratory syncytial virus (RSV) attachment and entry / Signaling by ERBB4 / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / positive regulation of peptidyl-serine phosphorylation / hair follicle development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / MAP kinase kinase kinase activity / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / embryonic placenta development / xenobiotic transport / salivary gland morphogenesis / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of MAPK cascade / sperm end piece / Signaling by ERBB2 / phosphotyrosine residue binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in EGFR signaling / transmembrane receptor protein tyrosine kinase activity / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / sperm principal piece / ossification / basal plasma membrane / cellular response to epidermal growth factor stimulus / epithelial cell proliferation / positive regulation of DNA replication / positive regulation of DNA repair / positive regulation of epithelial cell proliferation / Signal transduction by L1 / positive regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / NOTCH3 Activation and Transmission of Signal to the Nucleus / cellular response to amino acid stimulus / cellular response to estradiol stimulus / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / EGFR downregulation / cell-cell adhesion / Constitutive Signaling by EGFRvIII / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / negative regulation of protein catabolic process / receptor tyrosine kinase binding / RING-type E3 ubiquitin transferase / positive regulation of miRNA transcription / SH3 domain binding / epidermal growth factor receptor signaling pathway / kinase binding / Downregulation of ERBB2 signaling / ruffle membrane / positive regulation of fibroblast proliferation / cell morphogenesis / positive regulation of protein phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / neuron differentiation / HCMV Early Events / actin filament binding / ubiquitin protein ligase activity / transmembrane signaling receptor activity / cell junction / positive regulation of canonical Wnt signaling pathway / sperm midpiece / PIP3 activates AKT signaling / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis
Similarity search - Function
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 / 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 / Transcription Elongation Factor S-II; Chain A / SH2 domain / Zinc finger, C3HC4 type (RING finger) / SHC Adaptor Protein / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Growth factor receptor cysteine-rich domain superfamily / Ring finger / : / Zinc finger RING-type profile. / SH2 domain superfamily / Zinc finger, RING-type / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Zinc finger, RING/FYVE/PHD-type / 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
NICKEL (II) ION / Epidermal growth factor receptor / E3 ubiquitin-protein ligase CBL-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsChaikuad, A. / Guo, K. / Cooper, C.D.O. / Ayinampudi, V. / Krojer, T. / Ugochukwu, E. / Muniz, J.R.C. / Vollmar, M. / Canning, P. / von Delft, F. ...Chaikuad, A. / Guo, K. / Cooper, C.D.O. / Ayinampudi, V. / Krojer, T. / Ugochukwu, E. / Muniz, J.R.C. / Vollmar, M. / Canning, P. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of Cbl-c (Cbl-3) TKB domain in complex with EGFR pY1069 peptide
Authors: Chaikuad, A. / Guo, K. / Cooper, C.D.O. / Ayinampudi, V. / Krojer, T. / Ugochukwu, E. / Muniz, J.R.C. / Vollmar, M. / Canning, P. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, ...Authors: Chaikuad, A. / Guo, K. / Cooper, C.D.O. / Ayinampudi, V. / Krojer, T. / Ugochukwu, E. / Muniz, J.R.C. / Vollmar, M. / Canning, P. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Bountra, C. / Bullock, A.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Signal transduction protein CBL-C
B: Signal transduction protein CBL-C
C: Epidermal growth factor receptor
D: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0848
Polymers74,9214
Non-polymers1634
Water5,080282
1
A: Signal transduction protein CBL-C
C: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5424
Polymers37,4612
Non-polymers822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-23 kcal/mol
Surface area15470 Å2
MethodPISA
2
B: Signal transduction protein CBL-C
D: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5424
Polymers37,4612
Non-polymers822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-25 kcal/mol
Surface area15440 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-61 kcal/mol
Surface area29140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.250, 90.250, 191.581
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNCYSCYS1AA11 - 324 - 25
211GLNGLNCYSCYS1BB11 - 324 - 25
121CYSCYSSERSER1AA32 - 4025 - 33
221CYSCYSSERSER1BB32 - 4025 - 33
131PROPROARGARG1AA41 - 6334 - 56
231PROPROARGARG1BB41 - 6334 - 56
141GLUGLUPROPRO4AA64 - 7057 - 63
241GLUGLUPROPRO4BB64 - 7057 - 63
151GLYGLYPROPRO1AA71 - 9964 - 92
251GLYGLYPROPRO1BB71 - 9964 - 92
161PHEPHEGLNGLN1AA111 - 330104 - 323
261PHEPHEGLNGLN1BB111 - 330104 - 323
171PROPROLEULEU1AA100 - 11093 - 103
271PROPROLEULEU1BB100 - 11093 - 103
112LEULEUARGARG1CC1066 - 10681 - 3
212LEULEUARGARG1DD1066 - 10681 - 3
122SERSERGLYGLY1CC1070 - 10755 - 10
222SERSERGLYGLY1DD1070 - 10755 - 10

NCS ensembles :
ID
1
2

-
Components

#1: Protein Signal transduction protein CBL-C / SH3-binding protein CBL-C / SH3-binding protein CBL-3 / RING finger protein 57


Mass: 36185.320 Da / Num. of mol.: 2 / Fragment: CBL N-terminal, UNP residues 9-323 / Mutation: A64E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBL3, CBLC, RNF57 / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: Q9ULV8
#2: Protein/peptide Epidermal growth factor receptor / Receptor tyrosine-protein kinase erbB-1 / Proto-oncogene c-ErbB-1


Mass: 1275.240 Da / Num. of mol.: 2 / Fragment: EGFR, UNP residues 1066-1076 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P00533
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 277.15 K / pH: 7.5
Details: 20% Jeffamine M-600, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC Q315 3X3 CCD / Detector: CCD / Date: May 26, 2010 / Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.52→49.45 Å / Num. obs: 29742 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.1
Reflection shellResolution: 2.52→2.66 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 2 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 1FBV CHAIN A

1fbv


Resolution: 2.52→49.45 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU B: 19.618 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1505 5.1 %RANDOM
Rwork0.214 ---
all0.255 29663 --
obs0.216 28157 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.68 Å21.34 Å20 Å2
2--2.68 Å20 Å2
3----4.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.253 Å
Refinement stepCycle: LAST / Resolution: 2.52→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5163 0 4 282 5449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215358
X-RAY DIFFRACTIONr_bond_other_d0.0020.023708
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9727260
X-RAY DIFFRACTIONr_angle_other_deg1.1738949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.7085.118678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3322.571245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61515831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.521550
X-RAY DIFFRACTIONr_chiral_restr0.0720.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216008
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021146
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.321.53316
X-RAY DIFFRACTIONr_mcbond_other0.11.51338
X-RAY DIFFRACTIONr_mcangle_it0.54625285
X-RAY DIFFRACTIONr_scbond_it1.16232042
X-RAY DIFFRACTIONr_scangle_it1.5734.51969
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A4251TIGHT POSITIONAL0.040.05
1A64MEDIUM POSITIONAL0.010.5
1A4251TIGHT THERMAL0.040.5
1A64MEDIUM THERMAL0.022
2C114TIGHT POSITIONAL0.010.05
2C114TIGHT THERMAL0.020.5
LS refinement shellResolution: 2.52→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 99 -
Rwork0.337 2084 -
obs--99.95 %
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)
17.6107-3.25772.95387.8327-3.17277.5313-0.12950.2645-0.75760.307-0.0682-0.69660.28420.35170.19770.20770.0242-0.00960.2078-0.0450.24579.647240.35343.7005
26.18488.62462.811914.51146.46243.9505-0.5123-0.31980.8656-1.85880.15760.9235-1.43320.36410.35470.8477-0.0141-0.15470.4649-0.07520.65212.264960.207335.1401
33.1022-0.2586-0.34866.12570.81438.63820.0691-0.1628-0.24230.4461-0.0064-0.03110.37960.0071-0.06270.0549-0.0078-0.0310.1439-0.01110.07521.325941.6340
40.2976-1.9435-0.520723.57182.32271.0320.2361-0.06640.34211.6670.139-4.147-0.7490.0654-0.37511.16120.0186-0.32721.0044-0.06360.84998.596263.020928.2185
52.4219-0.42670.55871.17890.77351.65840.00970.0657-0.0673-0.0226-0.01610.120.0562-0.17450.00640.1409-0.03750.01990.1787-0.00360.0328-9.925438.665525.5468
63.8586-0.38671.47083.9917-0.04493.0189-0.04070.270.4659-0.336-0.17590.1039-0.5571-0.08330.21660.25860.0696-0.02230.2188-0.01880.1776-16.406857.076521.6195
71.27663.19671.31198.85213.35761.5613-0.0921-0.14190.4530.0377-0.21720.8403-0.1845-0.28310.30920.3110.0926-0.05970.4222-0.03440.3478-26.915250.647517.3411
86.63851.58730.25515.00922.86565.754-0.2588-0.1336-0.6972-0.10780.0840.5780.4538-0.32340.17480.229-0.0176-0.02440.21250.05040.2097-9.659140.3668-12.509
93.3329-6.10013.804811.702-7.42154.7463-0.650.30610.66671.79520.0238-0.8849-1.2553-0.11080.62621.01440.2571-0.01860.68640.1770.6424-2.263560.2289-3.9535
102.9642-0.2321-0.44926.34790.1028.81950.03050.3306-0.25-0.3463-0.01230.11410.4361-0.1821-0.01820.0477-0.0054-0.02990.1689-0.00270.0869-1.333341.6366-8.8054
117.77342.0996-5.78310.5925-1.56234.30310.97831.08932.14490.03590.43330.725-0.581-0.8157-1.41161.64720.1153-0.70870.65970.01681.4831-8.565363.00692.8742
122.29940.33490.42771.2705-0.61111.8539-0.014-0.0415-0.07520.0566-0.0056-0.07920.06090.18690.01960.13680.030.01180.16760.00720.0419.92938.66675.6403
134.00330.67581.87534.31360.31442.8503-0.1015-0.24710.44930.2981-0.1094-0.1578-0.67450.12890.21090.301-0.0611-0.02950.21660.02290.160516.412957.08189.5686
141.395-3.47671.72828.749-4.3362.293-0.0570.14740.39730.0365-0.2446-0.8821-0.14650.32080.30160.3815-0.1609-0.02680.53590.0070.407826.923350.649713.8417
1551.01782.7342.88313.1312-1.352111.9261-0.5356-0.24052.32951.05930.06681.7128-1.1709-1.09990.46880.6510.2070.08740.4392-0.1150.3984-23.931158.705229.8097
1637.62892.6199-0.77117.53739.38112.1629-0.26620.07070.7599-1.39920.9606-0.601-1.67221.2242-0.69440.619-0.18210.20890.60310.2140.6924.068958.53151.445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 26
2X-RAY DIFFRACTION2A27 - 42
3X-RAY DIFFRACTION3A43 - 94
4X-RAY DIFFRACTION4A95 - 110
5X-RAY DIFFRACTION5A111 - 238
6X-RAY DIFFRACTION6A239 - 278
7X-RAY DIFFRACTION7A279 - 330
8X-RAY DIFFRACTION8B10 - 26
9X-RAY DIFFRACTION9B27 - 42
10X-RAY DIFFRACTION10B43 - 94
11X-RAY DIFFRACTION11B95 - 110
12X-RAY DIFFRACTION12B111 - 238
13X-RAY DIFFRACTION13B239 - 278
14X-RAY DIFFRACTION14B279 - 330
15X-RAY DIFFRACTION15C1066 - 1075
16X-RAY DIFFRACTION16D1066 - 1075

+
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