[English] 日本語
Yorodumi
- PDB-4z7o: Integrin alphaIIbbeta3 in complex with AGDV peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z7o
TitleIntegrin alphaIIbbeta3 in complex with AGDV peptide
Components
  • (Monoclonal antibody 10E5 Fab ...) x 2
  • Integrin alpha-IIb
  • Integrin beta-3
  • Tetrapeptide ALA-GLY-ASP-VAL
KeywordsMembrane protein/Immune system / CELL ADHESION / PLATELET AGGREGATION / Membrane protein-Immune system complex
Function / homology
Function and homology information


tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / fibrinogen binding / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-PKCalpha complex / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / blood coagulation, fibrin clot formation / negative regulation of lipid transport / glycinergic synapse / angiogenesis involved in wound healing / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / cell-substrate junction assembly / filopodium membrane / positive regulation of vascular endothelial growth factor receptor signaling pathway / extracellular matrix binding / positive regulation of fibroblast migration / apolipoprotein A-I-mediated signaling pathway / regulation of postsynaptic neurotransmitter receptor internalization / regulation of bone resorption / positive regulation of cell adhesion mediated by integrin / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / positive regulation of leukocyte migration / Molecules associated with elastic fibres / smooth muscle cell migration / positive regulation of cell-matrix adhesion / cell adhesion mediated by integrin / microvillus membrane / negative chemotaxis / Syndecan interactions / cellular response to insulin-like growth factor stimulus / activation of protein kinase activity / p130Cas linkage to MAPK signaling for integrins / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / cellular response to platelet-derived growth factor stimulus / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / negative regulation of macrophage derived foam cell differentiation / fibronectin binding / negative regulation of lipid storage / ECM proteoglycans / positive regulation of bone resorption / positive regulation of T cell migration / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / coreceptor activity / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / embryo implantation / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / positive regulation of smooth muscle cell proliferation / wound healing / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet activation / platelet aggregation / VEGFA-VEGFR2 Pathway / cell-cell adhesion / ruffle membrane / cellular response to mechanical stimulus / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants
Similarity search - Function
ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : ...ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / 7 Propeller / Methylamine Dehydrogenase; Chain H / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å
AuthorsLin, F.Y. / Zhu, J. / Springer, T.A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: beta-Subunit Binding Is Sufficient for Ligands to Open the Integrin alpha IIb beta 3 Headpiece.
Authors: Lin, F.Y. / Zhu, J. / Eng, E.T. / Hudson, N.E. / Springer, T.A.
History
DepositionApr 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_conn_type / 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.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _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_label_asym_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-IIb
B: Integrin beta-3
C: Integrin alpha-IIb
D: Integrin beta-3
E: Monoclonal antibody 10E5 Fab heavy chain
F: Monoclonal antibody 10E5 Fab light chain
H: Monoclonal antibody 10E5 Fab heavy chain
L: Monoclonal antibody 10E5 Fab light chain
G: Tetrapeptide ALA-GLY-ASP-VAL
I: Tetrapeptide ALA-GLY-ASP-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,16934
Polymers297,24410
Non-polymers3,92524
Water10,521584
1
A: Integrin alpha-IIb
B: Integrin beta-3
H: Monoclonal antibody 10E5 Fab heavy chain
L: Monoclonal antibody 10E5 Fab light chain
G: Tetrapeptide ALA-GLY-ASP-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,69617
Polymers148,6225
Non-polymers2,07412
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Integrin alpha-IIb
D: Integrin beta-3
E: Monoclonal antibody 10E5 Fab heavy chain
F: Monoclonal antibody 10E5 Fab light chain
I: Tetrapeptide ALA-GLY-ASP-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,47317
Polymers148,6225
Non-polymers1,85112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)259.918, 144.524, 104.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Integrin alpha-IIb / GPalpha IIb / GPIIb / Platelet membrane glycoprotein IIb


Mass: 49357.805 Da / Num. of mol.: 2 / Fragment: UNP residues 32-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B, GP2B, ITGAB / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08514
#2: Protein Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 51804.625 Da / Num. of mol.: 2 / Fragment: UNP residues 29-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05106

-
Protein/peptide , 1 types, 2 molecules GI

#5: Protein/peptide Tetrapeptide ALA-GLY-ASP-VAL


Mass: 360.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Antibody , 2 types, 4 molecules EHFL

#3: Antibody Monoclonal antibody 10E5 Fab heavy chain


Mass: 23766.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody Monoclonal antibody 10E5 Fab light chain


Mass: 23332.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

-
Sugars , 4 types, 6 molecules

#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#12: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 5 types, 602 molecules

#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#10: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#11: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#13: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 11% PEG 8000, 0.2 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 92354 / % possible obs: 99.6 % / Redundancy: 3.7 % / Net I/σ(I): 2.68

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.85→49.027 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 1966 2.17 %
Rwork0.2232 --
obs0.2239 90699 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→49.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20760 0 225 584 21569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621635
X-RAY DIFFRACTIONf_angle_d0.55529371
X-RAY DIFFRACTIONf_dihedral_angle_d8.66912890
X-RAY DIFFRACTIONf_chiral_restr0.0433278
X-RAY DIFFRACTIONf_plane_restr0.0033806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8499-2.92120.41761120.39755041X-RAY DIFFRACTION78
2.9212-3.00020.41651350.38365876X-RAY DIFFRACTION92
3.0002-3.08840.4021400.38516388X-RAY DIFFRACTION99
3.0884-3.18810.39571410.34616395X-RAY DIFFRACTION100
3.1881-3.3020.33541420.31656415X-RAY DIFFRACTION100
3.302-3.43420.30351430.28296406X-RAY DIFFRACTION100
3.4342-3.59050.26491420.26356417X-RAY DIFFRACTION100
3.5905-3.77970.29381430.24746424X-RAY DIFFRACTION100
3.7797-4.01640.2421430.21766486X-RAY DIFFRACTION100
4.0164-4.32630.22541430.18826468X-RAY DIFFRACTION100
4.3263-4.76140.20361440.15976491X-RAY DIFFRACTION100
4.7614-5.44960.17181440.16476520X-RAY DIFFRACTION100
5.4496-6.86290.23741470.20366609X-RAY DIFFRACTION100
6.8629-49.03420.25591470.19816797X-RAY DIFFRACTION99
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)
15.5099-1.639-1.78272.77710.13894.2189-0.12930.28270.0689-0.20570.16720.08010.2199-0.3505-0.00690.74870.00410.02390.63930.02690.698148.937488.325938.7782
26.0962-2.7237-3.25028.57925.85524.67210.62590.51070.3045-1.2553-0.70010.4464-1.0149-0.9709-0.15440.92210.0924-0.02790.77290.13090.801540.594295.427339.0308
32.92540.0961-0.11771.39980.15131.78960.1103-0.23510.06850.399-0.13760.32260.1147-0.3360.0320.8036-0.03030.15660.6059-0.01370.768442.375994.895262.802
43.82661.6135-0.64226.34651.38255.95080.2673-0.3186-0.09350.5557-0.1386-0.39670.33270.374-0.1450.70650.09470.04680.47860.09080.594166.63985.595860.182
52.49940.7077-0.1491.86810.3152.9307-0.0577-0.072-0.37140.24010.0225-0.14190.32070.10450.01290.78410.0880.08020.49710.0370.713162.720182.896245.5798
67.0125-1.77462.25035.8088-4.69774.81552.23082.81640.8473-2.8226-3.4051-2.01381.51170.67770.72561.07130.17560.26450.7435-0.00870.879760.000872.887233.0186
77.6895-4.6013-4.33514.89452.98692.6585-0.3507-0.00020.16550.51180.7219-1.20120.65631.7644-0.25791.2170.3751-0.01512.7088-0.16411.7895122.950689.061935.4175
83.0609-2.8515-2.64136.62526.66269.32710.0375-0.4321.0053-0.36450.9239-1.1067-0.63131.4343-1.19021.0969-0.2084-0.03181.6858-0.00051.5354103.7106113.241252.256
92.39820.99760.11173.72140.52932.0840.0963-0.30270.31030.2071-0.0031-0.1197-0.42050.1188-0.08980.85610.02310.08350.5194-0.00570.763568.0224117.824763.3943
107.6062-6.0968-6.78337.61256.10276.004-1.012-0.5583-0.1010.91360.74810.23611.34881.46760.33091.0390.1759-01.28160.10861.373797.5314103.883760.4624
114.980.3584-2.35253.84953.79579.1694-0.12390.06390.12960.03840.0432-0.0930.64090.88910.10070.9720.0542-0.04491.4270.11071.3886100.7373104.268348.2019
123.79082.087-1.62093.9741-2.56433.714-0.1019-0.6206-0.3227-1.1906-0.3009-0.93370.75541.12360.23781.39070.41650.16732.7706-0.03611.4919116.224188.526719.0174
135.72841.2466-2.72285.5966-1.84615.3527-0.0601-0.10160.11920.06060.1309-0.31890.32191.0625-0.06280.81610.08960.04861.0539-0.0160.752688.17294.5747131.7442
143.5310.4623-0.36731.3653-0.37582.7015-0.22240.8693-0.1291-0.4085-0.0899-0.30420.37390.57330.32921.05170.15320.25691.44010.01550.892592.380290.0347107.4822
156.019-2.0431-1.14663.66350.56815.6139-0.16721.0556-0.8752-0.5648-0.06950.05251.4168-0.37340.26981.4368-0.08310.27871.0162-0.23180.962571.749475.7193115.2614
164.084-0.77740.19422.74340.12754.174-0.2215-0.0547-0.8734-0.27620.2176-0.19021.08590.0730.02931.1630.01940.21810.8954-0.11570.932773.104576.2788126.1772
175.2899-0.0616-0.17984.3433-0.81354.6012-0.51790.2448-0.486-0.00910.10890.01780.8727-0.05590.39490.91460.04280.08630.94930.00290.727675.83284.7284132.4602
184.4223-3.20881.62138.5688-4.08446.0212-0.0072-0.3155-0.32440.8051-0.2198-0.33760.38260.34810.23420.81550.02630.15120.9804-0.05410.766882.2285.5692136.8298
197.68911.2031-5.57717.1701-1.57994.1725-0.84760.7972-0.7882-0.28380.28011.24782.0941-1.70770.87491.6892-0.64870.34552.0513-0.12451.717315.931569.3059141.4911
204.08341.253-2.66711.226-1.20563.6447-0.15081.49280.4696-0.24690.3920.4210.3171-1.4256-0.28341.216-0.2532-0.09031.89190.150.973844.593698.3222105.2271
213.85590.25640.22492.1408-0.54164.4439-0.23091.16650.4322-0.47160.27170.0860.0166-0.7994-0.02691.0083-0.1091-0.00261.59990.17550.791660.7631100.5633101.5377
224.57220.4082-1.11892.8166-0.18426.0355-0.50441.1612-0.4202-0.0557-0.12240.1521.1218-0.78310.54551.3582-0.42310.04351.84-0.08321.063733.417484.3047118.6267
239.71492.81523.91349.72924.00142.8445-0.73030.0159-0.27010.5765-0.53360.13152.2165-2.15471.21481.6548-0.24870.29521.65620.01591.406720.428479.1396157.2602
246.26750.76160.33224.8204-4.79634.94440.66140.4854-4.23191.38941.40780.81772.6138-2.5311-1.68091.3396-0.4590.06671.6910.57422.87129.640872.5271159.1869
254.2672-2.20362.23815.97260.10461.4749-0.13260.8066-1.2157-0.9698-0.68840.33811.48091.52880.82621.61520.23190.45941.87810.05571.6952120.801682.638483.8939
262.0852-0.2404-0.90496.84121.76020.791-0.0862.77210.4585-2.6441-0.27540.5720.9742-0.28650.43092.59750.05040.0742.8629-0.19861.1813116.116884.895578.501
275.4748-2.298-0.75072.2412.24873.2350.5970.43960.7234-1.0441-0.5681-0.07510.80280.01370.04751.36730.05420.37382.2690.30361.258112.659893.014987.9964
284.8859-0.5473-1.92713.71440.53484.7928-0.1051.28430.0074-0.7048-0.2955-0.28241.0760.10710.18191.39330.16010.4352.31210.13121.2743115.9689.721485.7789
292.3974-1.6836-1.966.5645-0.08522.4874-0.37440.74380.1209-0.8466-0.0381-1.86070.69610.4370.45841.95730.46690.36343.04580.21872.0499150.015582.579279.9806
302.3255-0.49882.17623.09531.28343.31411.58282.30770.30820.1912-0.6442-0.14470.83391.3631-1.00751.97811.06410.27783.56320.11262.0222151.108281.278979.653
317.2861-1.50672.55814.9357-1.65445.9850.1850.61041.46540.1934-0.8065-1.1908-0.59621.1430.49041.3162-0.06540.29941.92730.23751.907126.9072107.25296.1477
327.2952-3.4141-0.11282.4198-1.18366.38060.04870.05582.56650.6852-0.0908-1.09770.47750.7869-0.01740.92360.0056-0.09162.10820.13012.0024133.7464102.6526106.7312
335.4945-2.62810.96843.2705-0.03132.2996-0.2402-0.25120.84940.14130.0056-0.84830.26880.86290.27311.1689-0.01780.24752.22580.12381.3891122.792198.6756102.4199
344.67060.8629-4.30350.2208-0.85774.0403-0.670.6040.6243-0.3938-1.0144-0.39790.53442.44561.3281.24060.33120.34533.83430.2472.1269150.735597.259894.9214
353.16040.0993-0.03054.4030.90134.04540.23370.90920.2267-0.9757-0.2152-0.44-0.39212.2039-0.13252.08690.31910.56723.16990.4212.0937152.416997.738778.7008
361.42041.1836-0.79881.47470.41444.01180.06821.20880.101-0.87770.379-0.9929-0.2820.6132-0.39481.65350.06170.64913.73610.4512.4767156.460998.503180.1195
378.8291-3.8024-5.96312.50323.23768.9208-0.4446-0.9331-0.18331.28950.3664-0.0541.34350.4170.35461.4628-0.04950.20391.54090.01941.170119.368889.910285.8022
384.02812.97522.19574.4218-0.30243.8761-0.0723-0.77240.73940.28540.15270.4312-0.24490.0535-0.13080.95690.03810.1751.197-0.15411.095918.0113101.729980.0463
399.2424-0.19-3.87542.2074-0.64454.54580.0592-0.97050.17430.94960.09250.4381-0.1128-0.3056-0.14771.0660.03080.26471.2588-0.03641.005117.361896.062683.3068
408.55871.64772.93764.09772.84955.2709-0.0462-1.1426-1.77290.74740.07210.68130.8805-0.0098-0.00261.32070.04780.22941.51130.57682.2243-17.41283.897594.1014
419.37097.55643.96046.47412.02034.8653-0.2169-0.1389-2.84080.12830.3952-0.6430.7110.6057-0.27621.00310.2450.30241.63520.22612.5531-8.68882.706689.8095
425.28752.08892.04180.96681.7956.65020.295-0.2148-2.41120.2924-0.07140.00211.4916-0.3743-0.23821.4433-0.0060.1881.49920.6252.9166-16.037877.631593.5091
435.29962.84950.68566.83360.61061.0255-0.07020.80011.24140.0106-0.19551.98920.0104-0.76440.15390.91340.0640.17191.63-0.25621.67312.082100.203963.2242
445.49830.5199-0.68453.90540.18563.5344-0.08590.4685-0.6128-0.0873-0.1130.75990.2321-0.90720.25660.8388-0.0750.09271.2758-0.17471.148912.000994.076963.2313
456.60962.451.33175.23621.38293.6421-0.06150.1952-0.27860.1393-0.25041.15210.3-1.18860.35670.832-0.02410.16171.4781-0.14211.34976.015595.187166.5149
464.4889-0.11691.05031.75971.78894.8353-0.3971-0.087-1.5310.26980.05490.41030.61230.19350.44820.9687-0.00540.23591.50370.13762.0041-20.145689.281883.8499
476.6583-1.7693-0.15481.66060.7834.4468-0.1295-1.1536-1.7664-0.36650.46820.1912-0.4910.5233-0.20150.8631-0.09760.18881.37490.38081.7642-17.771394.450784.3208
484.82160.9378-0.58083.16052.18356.0317-0.008-0.4472-0.94290.5693-0.35130.84830.1995-1.59760.4071.00850.09650.33811.69550.18621.8995-29.076295.280588.9322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:44)
2X-RAY DIFFRACTION2(chain A and resid 45:73)
3X-RAY DIFFRACTION3(chain A and resid 74:274)
4X-RAY DIFFRACTION4(chain A and resid 275:334)
5X-RAY DIFFRACTION5(chain A and resid 335:448)
6X-RAY DIFFRACTION6(chain A and resid 449:454)
7X-RAY DIFFRACTION7(chain B and resid 3:62)
8X-RAY DIFFRACTION8(chain B and resid 63:108)
9X-RAY DIFFRACTION9(chain B and resid 109:349)
10X-RAY DIFFRACTION10(chain B and resid 350:390)
11X-RAY DIFFRACTION11(chain B and resid 391:432)
12X-RAY DIFFRACTION12(chain B and resid 433:466)
13X-RAY DIFFRACTION13(chain C and resid 1:68)
14X-RAY DIFFRACTION14(chain C and resid 69:274)
15X-RAY DIFFRACTION15(chain C and resid 275:334)
16X-RAY DIFFRACTION16(chain C and resid 335:399)
17X-RAY DIFFRACTION17(chain C and resid 400:428)
18X-RAY DIFFRACTION18(chain C and resid 429:453)
19X-RAY DIFFRACTION19(chain D and resid 3:50)
20X-RAY DIFFRACTION20(chain D and resid 51:176)
21X-RAY DIFFRACTION21(chain D and resid 177:353)
22X-RAY DIFFRACTION22(chain D and resid 354:440)
23X-RAY DIFFRACTION23(chain D and resid 441:465)
24X-RAY DIFFRACTION24(chain D and resid 466:471)
25X-RAY DIFFRACTION25(chain E and resid 1:15)
26X-RAY DIFFRACTION26(chain E and resid 16:22)
27X-RAY DIFFRACTION27(chain E and resid 23:64)
28X-RAY DIFFRACTION28(chain E and resid 65:119)
29X-RAY DIFFRACTION29(chain E and resid 120:170)
30X-RAY DIFFRACTION30(chain E and resid 171:219)
31X-RAY DIFFRACTION31(chain F and resid 1:11)
32X-RAY DIFFRACTION32(chain F and resid 12:24)
33X-RAY DIFFRACTION33(chain F and resid 25:102)
34X-RAY DIFFRACTION34(chain F and resid 103:118)
35X-RAY DIFFRACTION35(chain F and resid 119:164)
36X-RAY DIFFRACTION36(chain F and resid 165:214)
37X-RAY DIFFRACTION37(chain H and resid 1:31)
38X-RAY DIFFRACTION38(chain H and resid 32:64)
39X-RAY DIFFRACTION39(chain H and resid 65:120)
40X-RAY DIFFRACTION40(chain H and resid 121:151)
41X-RAY DIFFRACTION41(chain H and resid 152:179)
42X-RAY DIFFRACTION42(chain H and resid 180:219)
43X-RAY DIFFRACTION43(chain L and resid 1:27)
44X-RAY DIFFRACTION44(chain L and resid 28:71)
45X-RAY DIFFRACTION45(chain L and resid 72:106)
46X-RAY DIFFRACTION46(chain L and resid 107:145)
47X-RAY DIFFRACTION47(chain L and resid 146:182)
48X-RAY DIFFRACTION48(chain L and resid 183:214)

+
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