[English] 日本語
Yorodumi
- PDB-4o02: AlphaVBeta3 integrin in complex with monoclonal antibody FAB fragment. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o02
TitleAlphaVBeta3 integrin in complex with monoclonal antibody FAB fragment.
Components
  • 17E6 heavy chain
  • 17E6 light chain
  • Integrin alpha-V
  • Integrin beta-3
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / tube development ...integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / 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 / Laminin interactions / 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 / negative regulation of low-density lipoprotein receptor activity / fibrinogen binding / alphav-beta3 integrin-PKCalpha complex / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / regulation of phagocytosis / blood coagulation, fibrin clot formation / mesodermal cell differentiation / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / glycinergic synapse / angiogenesis involved in wound healing / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / alphav-beta3 integrin-IGF-1-IGF1R complex / cell-substrate junction assembly / transforming growth factor beta binding / platelet-derived growth factor receptor binding / entry into host cell by a symbiont-containing vacuole / positive regulation of small GTPase mediated signal transduction / filopodium membrane / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of fibroblast migration / regulation of postsynaptic neurotransmitter receptor internalization / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / positive regulation of cell adhesion mediated by integrin / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / integrin complex / positive regulation of intracellular signal transduction / Molecules associated with elastic fibres / smooth muscle cell migration / cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / 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 / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / endodermal cell differentiation / 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 / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / positive regulation of bone resorption / positive regulation of T cell migration / Integrin cell surface interactions / vasculogenesis / voltage-gated calcium channel activity / negative regulation of endothelial cell apoptotic process / coreceptor activity / specific granule membrane / phagocytic vesicle / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of endothelial cell proliferation / embryo implantation / ERK1 and ERK2 cascade / Integrin signaling / positive regulation of endothelial cell migration / positive regulation of cell adhesion / cell-matrix adhesion
Similarity search - Function
Hormone receptor fold - #30 / ntegrin, alpha v. Chain A, domain 4 / Integrin domains. Chain A, domain 2 / Hormone receptor fold / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / 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 ...Hormone receptor fold - #30 / ntegrin, alpha v. Chain A, domain 4 / Integrin domains. Chain A, domain 2 / Hormone receptor fold / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / 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 / Laminin / Laminin / 7 Propeller / Methylamine Dehydrogenase; Chain H / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Ribbon / Few Secondary Structures / Irregular / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / NITRATE ION / Integrin beta-3 / Integrin alpha-V
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.605 Å
AuthorsMahalingam, B. / van Agthoven, J. / Xiong, J. / Arnaout, M.A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Atomic basis for the species-specific inhibition of alpha V integrins by monoclonal antibody 17E6 is revealed by the crystal structure of alpha V beta 3 ectodomain-17E6 Fab complex.
Authors: Mahalingam, B. / Van Agthoven, J.F. / Xiong, J.P. / Alonso, J.L. / Adair, B.D. / Rui, X. / Anand, S. / Mehrbod, M. / Mofrad, M.R. / Burger, C. / Goodman, S.L. / Arnaout, M.A.
History
DepositionDec 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references / Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / 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 / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_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 / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-V
B: Integrin beta-3
L: 17E6 light chain
H: 17E6 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,04521
Polymers229,9044
Non-polymers6,14117
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.464, 266.988, 102.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Integrin alpha-V / Vitronectin receptor subunit alpha


Mass: 106375.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06756
#2: Protein Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 76523.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P05106

-
Antibody , 2 types, 2 molecules LH

#3: Antibody 17E6 light chain


Mass: 23706.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Antibody 17E6 heavy chain


Mass: 23298.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

-
Sugars , 6 types, 10 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-2/a4-b1_b4-c1_c3-d1_c6-e1_e4-f1WURCSPDB2Glycan 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]{[(4+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#8: 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.: 3
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
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-3DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_d3-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#10: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 2 types, 7 molecules

#11: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#12: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 13.5% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 31351 / % possible obs: 87.9 % / Observed criterion σ(I): 31351 / Redundancy: 3.8 % / Biso Wilson estimate: 112 Å2 / Rsym value: 0.131 / Net I/σ(I): 8.3
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1 / Rsym value: 0.866 / % possible all: 55.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.605→49.862 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 33.92 / Stereochemistry target values: ML / Details: RAMACHANDRAN RESTRAINS
RfactorNum. reflection% reflection
Rfree0.3118 1562 4.99 %
Rwork0.2465 --
obs0.2497 31286 87.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.605→49.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13132 0 394 0 13526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813859
X-RAY DIFFRACTIONf_angle_d1.37418980
X-RAY DIFFRACTIONf_dihedral_angle_d14.8894259
X-RAY DIFFRACTIONf_chiral_restr0.0512252
X-RAY DIFFRACTIONf_plane_restr0.0072573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6054-3.72180.3724870.32491635X-RAY DIFFRACTION54
3.7218-3.85470.3729990.31071988X-RAY DIFFRACTION65
3.8547-4.0090.3221150.28052236X-RAY DIFFRACTION74
4.009-4.19140.31911460.27042572X-RAY DIFFRACTION85
4.1914-4.41220.32361620.24052774X-RAY DIFFRACTION91
4.4122-4.68850.28121520.21612945X-RAY DIFFRACTION96
4.6885-5.05020.29131440.21263035X-RAY DIFFRACTION99
5.0502-5.55780.29121670.23693071X-RAY DIFFRACTION100
5.5578-6.36060.34831670.26483085X-RAY DIFFRACTION100
6.3606-8.00830.33951560.28263147X-RAY DIFFRACTION100
8.0083-49.86650.28841670.22343236X-RAY DIFFRACTION98
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)
14.64611.73373.06012.8360.92864.2343-0.22770.16570.4345-1.4185-0.12780.2979-0.3427-1.16540.3980.9356-0.14590.24580.8230.10942.1034-84.590856.9412-19.8699
22.4706-0.52360.34066.943-1.44043.7438-0.1598-0.34750.93420.6820.1247-0.5987-0.42390.1464-0.0040.46570.02890.0820.5496-0.09251.311-50.542459.61611.0595
35.44151.04642.50532.14120.76642.9640.15640.51850.4953-0.1381-0.35920.46830.0461-0.10320.15890.73330.17780.24530.57820.08071.5301-65.530759.1636-11.9175
47.29712.22771.34211.59181.19763.40680.18790.22250.2384-0.2272-0.02060.22790.00950.6688-0.19021.47260.3479-0.06711.91230.12021.6412-72.015244.9878-30.2976
50.42681.2377-1.533.671-4.53415.5863-0.1671-1.67-2.13121.1889-0.21960.30322.7815-0.39060.36884.2168-0.55330.07353.65051.81623.1122-40.357279.1169-28.7975
64.0444-1.54661.51193.8382-0.7174.30840.1571-0.8492-0.52040.1555-0.10970.6030.3985-0.0178-0.00920.5332-0.01720.01130.63660.05060.5891-42.742825.043417.5967
73.92221.34320.69734.1025-0.66315.48580.35910.6035-0.7171-0.97460.53870.67790.6866-0.5054-0.860.82620.013-0.21440.57450.12110.9045-51.101229.5331-4.6392
84.66411.58242.40030.78421.56893.32170.2640.25-1.323-1.7146-0.00841.07230.2311-0.6311-0.20742.015-0.0358-1.03341.1110.17082.1995-77.50315.6917-11.7723
91.71351.5146-0.04721.8456-2.16215.33220.34380.1917-0.0674-1.17220.50050.91551.8196-0.4331-0.79822.110.088-0.55050.969-0.02532.6647-78.13728.4029-27.8464
102.50431.0898-0.01215.1758-0.18733.4912-0.0976-0.3932-0.3149-1.22210.7286-1.17161.72020.1687-0.65522.72120.2606-0.42541.3731-0.10412.0989-65.046918.9114-42.1338
113.23861.43450.92014.72360.03310.2131-0.5780.1064-0.7854-1.37160.2333-2.33220.10240.49510.37931.953-0.02150.63512.5370.06992.517-26.921358.8388-41.7315
126.325-2.29490.00845.3840.02234.0639-1.2646-1.44960.98841.42130.0555-0.6805-0.11840.33031.17660.9264-0.1851-0.34851.57280.08860.8993-9.71823.767640.8371
138.9754-2.26650.60767.5961-0.00051.60840.22311.2723-1.3087-0.5518-0.43240.57040.42590.40070.14640.80220.23970.29071.0568-0.28261.2658-14.25918.208629.7929
145.3141-0.7989-0.51557.7402-1.21035.2222-0.2536-1.8548-0.32470.30780.21060.5129-0.4579-0.3771-0.04610.5295-0.0174-0.03671.2966-0.04770.7002-11.663321.708635.5388
153.49321.00511.15190.33660.34810.37860.3293-0.2312-1.26960.0186-0.5518-1.51630.54750.16840.22450.65550.0489-0.02441.86090.46422.426513.9317.508336.5198
164.8478-1.00341.85666.35261.13325.4382-0.27490.50840.554-0.2310.2433-1.9407-0.3163.008-0.10980.8822-0.0275-0.15422.1986-0.01931.744420.617814.837732.7426
173.44140.37831.20287.0884-1.79241.688-0.1504-1.0590.38670.7289-0.8928-2.5891-0.4210.37311.13571.0639-0.1373-0.15332.8708-0.09531.849530.058515.08335.821
182.094-0.37520.49694.2105-1.48695.47830.4010.89680.517-0.0855-0.8959-1.7248-0.31611.46380.48630.77570.04840.16621.06590.30981.6423-7.713232.51816.1715
197.127-1.8595-0.72033.693-0.33651.5418-0.4882-0.45070.5718-0.32510.2215-2.19250.7871.96190.23270.91770.61340.42262.51270.08322.296710.644917.557621.2372
204.01733.0861-0.26122.62160.89284.6763-0.95930.4343-0.659-0.30251.0036-0.10671.22241.117-0.04521.26670.52720.25782.5027-0.20271.74720.11439.127518.1597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 121 )
2X-RAY DIFFRACTION2chain 'B' and (resid 122 through 304 )
3X-RAY DIFFRACTION3chain 'B' and (resid 305 through 441 )
4X-RAY DIFFRACTION4chain 'B' and (resid 442 through 657 )
5X-RAY DIFFRACTION5chain 'B' and (resid 658 through 687 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1 through 214 )
7X-RAY DIFFRACTION7chain 'A' and (resid 215 through 403 )
8X-RAY DIFFRACTION8chain 'A' and (resid 404 through 533 )
9X-RAY DIFFRACTION9chain 'A' and (resid 534 through 622 )
10X-RAY DIFFRACTION10chain 'A' and (resid 623 through 742 )
11X-RAY DIFFRACTION11chain 'A' and (resid 743 through 953 )
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 32 )
13X-RAY DIFFRACTION13chain 'L' and (resid 33 through 61 )
14X-RAY DIFFRACTION14chain 'L' and (resid 62 through 102 )
15X-RAY DIFFRACTION15chain 'L' and (resid 103 through 120 )
16X-RAY DIFFRACTION16chain 'L' and (resid 121 through 173 )
17X-RAY DIFFRACTION17chain 'L' and (resid 174 through 214 )
18X-RAY DIFFRACTION18chain 'H' and (resid 1 through 98 )
19X-RAY DIFFRACTION19chain 'H' and (resid 99 through 150 )
20X-RAY DIFFRACTION20chain 'H' and (resid 151 through 218 )

+
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