[English] 日本語
Yorodumi
- PDB-6vel: Crystal Structure of Human E-cadherin bound by mouse monoclonal a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vel
TitleCrystal Structure of Human E-cadherin bound by mouse monoclonal antibody 66E8Fab
Components
  • 66E8 Fab Heavy Chain
  • 66E8 Fab Light Chain
  • Ubiquitin-like protein SMT3,Cadherin-1
KeywordsCELL ADHESION/Immune System / SSGCID / cadherin / E-cadherin / antibody / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / CELL ADHESION / CELL ADHESION-Immune System complex
Function / homology
Function and homology information


response to heparin / desmosome assembly / response to Gram-positive bacterium / pituitary gland development / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / gamma-catenin binding / SUMOylation of transcription factors ...response to heparin / desmosome assembly / response to Gram-positive bacterium / pituitary gland development / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / gamma-catenin binding / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of axon extension / desmosome / septin ring / SUMOylation of DNA damage response and repair proteins / cellular response to indole-3-methanol / Transcriptional and post-translational regulation of MITF-M expression and activity / calcium-dependent cell-cell adhesion / SUMOylation of DNA replication proteins / flotillin complex / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / cell-cell adhesion mediated by cadherin / adherens junction organization / Formation of definitive endoderm / catenin complex / SUMOylation of SUMOylation proteins / Apoptotic cleavage of cell adhesion proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cell-cell junction assembly / SUMOylation of RNA binding proteins / Adherens junctions interactions / GTPase activating protein binding / SUMOylation of chromatin organization proteins / ankyrin binding / negative regulation of cell-cell adhesion / cellular response to lithium ion / apical junction complex / homophilic cell-cell adhesion / ubiquitin-like protein ligase binding / protein sumoylation / lateral plasma membrane / Integrin cell surface interactions / RHO GTPases activate IQGAPs / synapse assembly / cell adhesion molecule binding / positive regulation of protein localization / Degradation of the extracellular matrix / Transcriptional and post-translational regulation of MITF-M expression and activity / InlA-mediated entry of Listeria monocytogenes into host cells / protein tyrosine kinase binding / negative regulation of cell migration / condensed nuclear chromosome / protein localization to plasma membrane / adherens junction / trans-Golgi network / cell-cell adhesion / beta-catenin binding / positive regulation of protein import into nucleus / response to toxic substance / cytoplasmic side of plasma membrane / protein tag activity / cell morphogenesis / neuron projection development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell junction / cell migration / lamellipodium / actin cytoskeleton / regulation of gene expression / postsynapse / endosome / cadherin binding / response to xenobiotic stimulus / calcium ion binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cadherin-1 / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Saccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Pnas Nexus / Year: 2022
Title: Regulation of multiple dimeric states of E-cadherin by adhesion activating antibodies revealed through Cryo-EM and X-ray crystallography.
Authors: Maker, A. / Bolejack, M. / Schecterson, L. / Hammerson, B. / Abendroth, J. / Edwards, T.E. / Staker, B. / Myler, P.J. / Gumbiner, B.M.
History
DepositionJan 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 2.0Aug 12, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_label_seq_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_prop.value / _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_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 / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.version / _struct_asym.entity_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_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_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _struct_site_gen.symmetry
Description: Sequence discrepancy / Details: Replaced incorrect Na ion with Ca / Provider: author / Type: Coordinate replacement
Revision 2.1Feb 1, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.4Oct 22, 2025Group: Structure summary / Category: audit_author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: 66E8 Fab Heavy Chain
L: 66E8 Fab Light Chain
C: Ubiquitin-like protein SMT3,Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,54112
Polymers88,8443
Non-polymers6979
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-137 kcal/mol
Surface area29380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.170, 142.170, 90.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11C-403-

SO4

21C-403-

SO4

-
Components

-
Protein , 1 types, 1 molecules C

#3: Protein Ubiquitin-like protein SMT3,Cadherin-1 / CAM 120/80 / Epithelial cadherin / E-cadherin / Uvomorulin


Mass: 36625.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Homo sapiens (human)
Strain: ATCC 204508 / S288c / Gene: SMT3, YDR510W, D9719.15, CDH1, CDHE, UVO / Plasmid: pET-21a_modified
Details (production host): N-term His/SUMO-tagged human E-cadherin subunits EC1-EC2 in pET-21a from Barry Gumbiner
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12306, UniProt: P12830

-
Antibody , 2 types, 2 molecules HL

#1: Antibody 66E8 Fab Heavy Chain


Mass: 26407.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET-21a_modified
Details (production host): plasmid: N-term His/SUMO-tagged human E-cadherin subunits EC1-EC2 in pET-21a from Barry Gumbiner
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Antibody 66E8 Fab Light Chain


Mass: 25810.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: LH
Details (production host): full Fab, mouse mAb 66E8, light chain; vector unknown; construct sequence significantly different from reference; from Gumbiner lab, Wei Wang
Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 3 types, 137 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: A complex of HosaA.19747.a.KW2, MumuA.20194.a.LG23, and MumuA.20195.a.LH23 was crystallized at 10.4 mg/ml at 14C and mixed 1:1 with 12.5% (w/v) PEG 4000, 20% (v/v) 1,2,6-hexanetriol, 0.1M ...Details: A complex of HosaA.19747.a.KW2, MumuA.20194.a.LG23, and MumuA.20195.a.LH23 was crystallized at 10.4 mg/ml at 14C and mixed 1:1 with 12.5% (w/v) PEG 4000, 20% (v/v) 1,2,6-hexanetriol, 0.1M GlyGly/AMPD pH 8.5, 0.03M of each Lithium sulfate, Sodium sulfate, and Potassium sulfate. Tray 307437a10: puck ckt8-9.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 18, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.65→46.54 Å / Num. obs: 30906 / % possible obs: 99.9 % / Redundancy: 8.734 % / Biso Wilson estimate: 60.262 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.065 / Χ2: 1.057 / Net I/σ(I): 24.68 / Num. measured all: 269932
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.728.9840.5953.5620150224422430.920.631100
2.72-2.798.9460.4474.7119798221322130.9580.473100
2.79-2.878.9790.3466.1519215214021400.9680.366100
2.87-2.968.9510.2647.8718726209220920.9830.28100
2.96-3.068.9720.19410.8818150202320230.9910.205100
3.06-3.178.8880.16113.1217304194719470.9920.171100
3.17-3.298.920.12616.1916940189918990.9960.133100
3.29-3.428.7840.09919.9715846180418040.9970.105100
3.42-3.578.7880.07525.915405175317530.9980.079100
3.57-3.758.720.06530.1214755169216920.9980.069100
3.75-3.958.6580.05634.413705158315830.9990.059100
3.95-4.198.5470.04739.9712897151015090.9990.0599.9
4.19-4.488.5110.0444.5312136142614260.9990.043100
4.48-4.848.4610.03847.0911295133513350.9990.04100
4.84-5.38.5170.03847.9810476123012300.9990.04100
5.3-5.938.4740.03746.989491112011200.9990.039100
5.93-6.848.4570.03548.1783729909900.9990.037100
6.84-8.388.3650.02952.3371358538530.9990.031100
8.38-11.858.0420.02356.64539667167110.025100
11.85-46.547.1540.02354.3927403993830.9990.02596

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2o72

2o72


Resolution: 2.65→46.54 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 1542 4.99 %
Rwork0.194 29330 -
obs0.1961 30872 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 218.3 Å2 / Biso mean: 74.6742 Å2 / Biso min: 36.85 Å2
Refinement stepCycle: final / Resolution: 2.65→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 33 128 4884
Biso mean--117.65 56.83 -
Num. residues----630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.65-2.740.31341570.279126322789
2.74-2.830.31551220.251926272749
2.83-2.950.26891340.254126492783
2.95-3.080.30171300.240226362766
3.08-3.240.24831500.237926602810
3.24-3.450.2681690.219226012770
3.45-3.710.2541310.207526532784
3.71-4.090.23331420.186526792821
4.09-4.680.19191300.148726882818
4.68-5.890.18741390.162227082847
5.89-46.540.23191380.183727972935
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)
12.0286-0.3195-0.41987.11630.69482.78160.1496-0.01260.30320.0652-0.0126-0.032-0.2598-0.0048-0.15140.40160.01510.07640.4238-0.0030.3189-60.719550.881611.0364
25.92251.36521.20228.97121.01692.23260.3130.75010.5154-0.18140.23760.5979-1.2001-1.38-0.56650.96430.24450.27880.80880.21430.7685-61.669276.5386-13.2612
32.26650.0949-0.31144.5958-1.38675.81010.1550.45850.5163-0.19440.50210.6917-1.3723-0.9691-0.60.9180.22150.21260.89860.2310.8061-63.092375.6493-14.7998
43.29070.41190.39624.7505-2.14887.61510.00660.27480.1581-0.2129-0.0106-0.17330.0840.29070.02120.29360.01910.03450.3515-0.03660.3006-49.753840.3831-6.5177
51.30190.2588-0.61560.37650.46441.40.2499-0.00820.47640.260.18470.0609-1.02220.0673-0.38560.7111-0.05520.13810.3998-0.00520.5111-50.597562.2723-9.566
63.59390.3747-0.68429.07291.79356.23760.4834-0.22630.66661.1110.53430.2115-1.14890.3865-0.86080.8128-0.18240.22990.6219-0.04080.6912-46.785670.5925-15.2492
71.3970.26750.65222.5154-0.73450.54730.480.05941.50660.03130.6057-0.6882-1.91560.7579-0.57271.5389-0.40960.47610.6784-0.0741.3038-43.457180.5537-17.2175
86.14820.6877-1.55313.1036-0.36622.5170.49012.2589-0.7806-0.0464-0.0258-0.8059-0.23620.565-0.45940.6150.2324-0.03281.2289-0.280.8857-17.673622.89695.3579
96.67321.4175-1.75650.79290.44312.5-0.30.5341-1.22840.17020.2487-0.41640.49140.31220.12260.71920.1308-0.09290.4382-0.08590.6194-41.931518.660812.9592
102.48260.6113-2.56622.3324-0.43953.16910.10480.22590.02580.39920.03870.1890.5301-0.3565-0.15990.6801-0.0330.00350.44010.00620.3452-65.816524.87520.0299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 20 through 141 )H20 - 141
2X-RAY DIFFRACTION2chain 'H' and (resid 142 through 179 )H142 - 179
3X-RAY DIFFRACTION3chain 'H' and (resid 180 through 235 )H180 - 235
4X-RAY DIFFRACTION4chain 'L' and (resid 20 through 109 )L20 - 109
5X-RAY DIFFRACTION5chain 'L' and (resid 110 through 147 )L110 - 147
6X-RAY DIFFRACTION6chain 'L' and (resid 148 through 193 )L148 - 193
7X-RAY DIFFRACTION7chain 'L' and (resid 194 through 229 )L194 - 229
8X-RAY DIFFRACTION8chain 'C' and (resid 102 through 173 )C102 - 173
9X-RAY DIFFRACTION9chain 'C' and (resid 174 through 247 )C174 - 247
10X-RAY DIFFRACTION10chain 'C' and (resid 248 through 314 )C248 - 314

+
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