[English] 日本語
Yorodumi
- PDB-7ukt: Integrin alpha IIB beta3 complex with BMS4.2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ukt
TitleIntegrin alpha IIB beta3 complex with BMS4.2
Components
  • 10E5 Fab heavy chain
  • 10E5 Fab light chain
  • Integrin alpha-IIb heavy chain
  • Isoform Beta-3C of Integrin beta-3
KeywordsCELL ADHESION/INHIBITOR / Complex / Inhibitor / BLOOD CLOTTING / CELL ADHESION / CELL ADHESION-INHIBITOR 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 / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization ...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 / maintenance of postsynaptic specialization structure / 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 / glycinergic synapse / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / angiogenesis involved in wound healing / platelet-derived growth factor receptor binding / alphav-beta3 integrin-IGF-1-IGF1R complex / filopodium membrane / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of fibroblast migration / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / positive regulation of cell adhesion mediated by integrin / positive regulation of leukocyte migration / apoptotic cell clearance / activation of protein kinase activity / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / Molecules associated with elastic fibres / smooth muscle cell migration / positive regulation of cell-matrix adhesion / cell adhesion mediated by integrin / negative chemotaxis / Syndecan interactions / cellular response to insulin-like growth factor stimulus / microvillus membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of osteoblast proliferation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / 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 / negative regulation of endothelial cell apoptotic process / coreceptor activity / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / Integrin signaling / embryo implantation / substrate adhesion-dependent cell spreading / protein kinase C binding / cell-matrix adhesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / wound healing / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cell-cell adhesion / platelet activation / platelet aggregation / VEGFA-VEGFR2 Pathway / ruffle membrane / cellular response to mechanical stimulus / positive regulation of fibroblast proliferation / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / Signaling by RAF1 mutants
Similarity search - Function
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 beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, tail / Integrin beta tail domain superfamily ...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 beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / 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 / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Chem-NJF / Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36994437552 Å
AuthorsLin, F.-Y. / Zhu, J. / Zhu, J. / Springer, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL-103526 United States
CitationJournal: Cell / Year: 2022
Title: A general chemical principle for creating closure-stabilizing integrin inhibitors.
Authors: Lin, F.Y. / Li, J. / Xie, Y. / Zhu, J. / Huong Nguyen, T.T. / Zhang, Y. / Zhu, J. / Springer, T.A.
History
DepositionApr 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 2, 2024Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-IIb heavy chain
B: Isoform Beta-3C of Integrin beta-3
C: Integrin alpha-IIb heavy chain
D: Isoform Beta-3C of Integrin beta-3
E: 10E5 Fab heavy chain
F: 10E5 Fab light chain
H: 10E5 Fab heavy chain
L: 10E5 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,63141
Polymers297,4068
Non-polymers5,22533
Water19,1321062
1
A: Integrin alpha-IIb heavy chain
B: Isoform Beta-3C of Integrin beta-3
H: 10E5 Fab heavy chain
L: 10E5 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,40920
Polymers148,7034
Non-polymers2,70616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Integrin alpha-IIb heavy chain
D: Isoform Beta-3C of Integrin beta-3
E: 10E5 Fab heavy chain
F: 10E5 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,22221
Polymers148,7034
Non-polymers2,51917
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)259.820, 144.370, 105.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Integrin alpha-IIb heavy chain


Mass: 49515.965 Da / Num. of mol.: 2 / Fragment: UNP Residues 32-488
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 Isoform Beta-3C of Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 52087.902 Da / Num. of mol.: 2 / Fragment: UNP Residues 27-498
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

-
Antibody , 2 types, 4 molecules EHFL

#3: 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: Mus musculus (house mouse)
#4: 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: Mus musculus (house mouse)

-
Sugars , 4 types, 6 molecules

#5: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#11: 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: obtained synthetically / 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 , 6 types, 1089 molecules

#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#9: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#12: Chemical ChemComp-NJF / (1-{[(5S)-3-(4-carbamimidoylphenyl)-4,5-dihydro-1,2-oxazol-5-yl]methyl}piperidin-4-yl)acetic acid


Mass: 344.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24N4O3 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1062 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.86 %
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

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36994437552→50 Å / Num. obs: 303038 / % possible obs: 99.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 66.5804951144 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.04
Reflection shellResolution: 2.37→2.43 Å / Num. unique obs: 11727 / CC1/2: 0.115

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T3P

3t3p


Resolution: 2.36994437552→49.036799364 Å / SU ML: 0.464094466934 / Cross valid method: FREE R-VALUE / σ(F): 0.913266545429 / Phase error: 30.336600776
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.218121107899 3789 1.25033824141 %
Rwork0.19385427248 299249 -
obs0.194166717043 303038 97.7598699279 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.904154425 Å2
Refinement stepCycle: LAST / Resolution: 2.36994437552→49.036799364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20715 0 306 1062 22083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0060199164063321715
X-RAY DIFFRACTIONf_angle_d0.50848972335229490
X-RAY DIFFRACTIONf_chiral_restr0.04184324154293280
X-RAY DIFFRACTIONf_plane_restr0.003652897783323816
X-RAY DIFFRACTIONf_dihedral_angle_d11.363385496512913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36994437552-2.39990.4213179302561400.40646043380111073X-RAY DIFFRACTION97.8702976346
2.3999-2.43150.4253895519221420.40458596624511113X-RAY DIFFRACTION97.9803255854
2.4315-2.46480.4335863745041410.39387545542511083X-RAY DIFFRACTION97.9492102278
2.4648-2.50.3983188987821410.38422618834811219X-RAY DIFFRACTION98.1171186733
2.5-2.53740.360468587641390.38138170899811038X-RAY DIFFRACTION98.0524607422
2.5374-2.5770.3751162843821390.36472628169911143X-RAY DIFFRACTION98.0020847811
2.577-2.61920.378533765231370.35280640240411121X-RAY DIFFRACTION97.7511504732
2.6192-2.66440.3583810377071410.34214298244810971X-RAY DIFFRACTION97.3711882229
2.6644-2.71290.3822827259241410.32810165535311093X-RAY DIFFRACTION97.780485682
2.7129-2.7650.3393483054171430.31811189966111107X-RAY DIFFRACTION97.7326035966
2.765-2.82150.3047859972871420.28924549296311139X-RAY DIFFRACTION98.1724828126
2.8215-2.88280.2899675811291400.27456640433711091X-RAY DIFFRACTION98.0787704131
2.8828-2.94990.3029147559811410.26031046738411130X-RAY DIFFRACTION98.128156016
2.9499-3.02360.2544755779971410.25346796339211104X-RAY DIFFRACTION97.9017934877
3.0236-3.10540.2800806741721400.24733715973811069X-RAY DIFFRACTION97.9037470521
3.1054-3.19670.2804690594921420.24487175739511132X-RAY DIFFRACTION97.7881863128
3.1967-3.29990.3335039123951370.22341235407811072X-RAY DIFFRACTION97.65638613
3.2999-3.41780.2975591786271390.21041702558611071X-RAY DIFFRACTION97.8526536313
3.4178-3.55460.1905014115161400.18723110088911107X-RAY DIFFRACTION97.9703832753
3.5546-3.71630.2203843327241320.17927661581411089X-RAY DIFFRACTION97.4891398784
3.7163-3.91220.2201615170081410.17083552001911090X-RAY DIFFRACTION97.8395330604
3.9122-4.15720.201426054731320.15387998610111011X-RAY DIFFRACTION97.4549588945
4.1572-4.47790.1685520354831460.138944432710963X-RAY DIFFRACTION96.7345872518
4.4779-4.92820.1565773084651460.13226574310311095X-RAY DIFFRACTION97.9181184669
4.9282-5.64040.1412949677661410.14320611433411109X-RAY DIFFRACTION98.013591218
5.6404-7.10290.1753453138881400.17296309556711042X-RAY DIFFRACTION97.2009735744
7.1029-49.0367993640.1585890449451450.14764274852710974X-RAY DIFFRACTION96.8048058506
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)
11.0448639377-0.136077161416-0.2133313007350.820749745554-0.3407520059050.6205913711460.0396879208610.1497863294280.0770704819613-0.0644748190277-0.03182885824350.06037634027410.0840251344021-0.2524717483444.5303215515E-60.6469384759660.05281737032980.04716554807990.5135661300770.04250402450210.63188597956946.746103797590.34175705838.4749699776
21.07823405577-0.364125546307-0.1855748604920.6457258378860.08940762923320.6749983780870.139072739856-0.1134357592370.02155954153860.278226149904-0.1708003656430.1408518027660.131980999878-0.1236877683663.58515981672E-70.602255063415-0.04933039037040.1396568427210.390038716382-0.008448584902330.56631594488544.694734963593.157897346262.6694654215
30.7010845389710.292243926806-0.01138394935541.097519479420.812666887681.35283271271-0.007721422701520.0352866425295-0.09151124910350.002625688323970.0377143701456-0.06614116497120.2459454628750.122975829027.82562000805E-60.5893640830080.06161674192480.06789162921130.3537807940710.05436550330480.52874042991864.622855802183.573529473847.8284605117
41.223428675630.01980596173680.2477740578590.817337686027-0.4563355213260.983072000346-0.06553357816510.08778270043010.3871875779550.2568429250740.355384464959-0.5749294693550.2098345646881.37167234215-0.00180019972070.5004606459580.15608081978-0.007826034766731.53062937705-0.0908815063750.930614024488113.844170445100.27071291743.4470220061
51.061097225430.343372714380.1052546843631.188736274620.4760280950450.5604742040570.0890529176108-0.09201141573220.1236822242160.138772511417-0.05234932953720.0340693409285-0.1733646119520.06120710350015.02018459086E-60.632023107748-0.01559342441360.07699195166130.3680590216820.007355347454710.56247202033868.8860424839117.18822702263.7789679859
60.443760788922-0.120000091603-0.4992630768690.1060063456080.1467589538210.373735878931-0.1764393077420.0820998103450.1029677636710.1472952231340.0434410203558-0.295364017050.3134084834330.8981793229-0.001149884462410.8343475267470.1928150363230.03591697191921.36792821092-0.04219041631721.03457227705105.40659705698.554793300442.4820446703
71.035397683770.406595793519-0.6446775613020.7086598151740.2074555422180.48543747146-0.213396318445-0.2571905287140.047282451209-0.0294748476422-0.0211181612417-0.1390774482960.1962421516670.561973660152-3.1501633325E-50.6321151172980.05479331344860.05258261578550.8563548914050.06992391792260.63686514904687.879353093194.3915215037132.349861798
82.078704240950.413529721157-0.62779895640.325095113821-0.5476733797631.61929891332-0.3936375456770.579189555924-0.182783517805-0.35991999430.0445710784405-0.1715538314860.4776043722270.440246990672-0.03665580679430.8086724256690.001420270077130.2015101982370.91241382929-0.005758818734670.63923812301690.168683365587.8280434779108.598527112
91.80825335410.155728968792-0.1595343200790.46265649982-0.3906391580421.77365266237-0.3672438283680.0440209924963-0.178841415922-0.04443876132040.101966953101-0.06085774560810.4793804276150.0127556934318-0.004128053972420.783986910450.01826081024570.1890245665830.5150945106990.00592880201220.59022625503373.355103561579.9207040134127.496852
100.0647870386303-0.03043597515150.02885555614810.1344444212850.03403080412540.015626928753-0.404939980848-0.00131876717168-0.328293532527-0.1430114096950.01035537796780.1536493129411.41096865416-0.767887804198-0.0001168081226211.31925049202-0.5663956938110.2654606017621.393091837350.001663063334021.1461167471617.721078866569.3655993289142.558082988
110.476086639288-0.225620331049-0.1141497300780.1306576464-0.1206559614160.237983010870.1811733412090.393636882580.4307880651620.08542166408170.07060900221470.74764295679-0.169283719266-1.15481214178-0.0968638251750.884537725862-0.403641545507-0.06250088414831.920295379080.1918285569981.0303961437919.679436201488.0395350605123.121391598
120.77483259939-0.4395831295620.1530570060940.4169248731870.6635941259521.17580716357-0.3480812283351.167468468130.324400277267-0.3655107993310.3809743191630.1073699291290.339924876971-0.750371314648-0.01914740622210.711684670116-0.32132999538-0.1834709786771.455626072150.3542435331880.55320299382144.596463755299.4082176664101.407257281
13-0.02937131858690.0692723344312-0.07149691475430.0205040341568-0.09977771187580.139900719196-0.6065932177631.013533926190.450666564212-0.5246610457980.384977216302-0.08546893193820.0758750862872-0.263972490104-0.002776677303060.826917747852-0.276198816472-0.02662504019721.203266269080.3211196663810.74661832818178.6354014098107.99987595297.1725000332
141.30915778432-0.4179717048990.3120725209470.838231123917-0.5674744606321.79666992044-0.3054327565640.7937753707720.386254748762-0.1931842239470.3049555266270.005350224477950.107355400286-0.4105015700030.1065591505590.672126583193-0.254933847248-0.03502976371921.052103622260.21733083250.57872379579460.3687739963100.876468352103.620905655
151.08557457719-1.26399096015-0.2255226566681.545337051890.2266762756670.502725938677-0.4136881813850.72257680221-0.319406184272-0.06910209787660.20545437057-0.004491351226540.0764877155587-0.183563188522-0.3728542917950.816490809463-0.526389168696-0.1530036846421.581890833480.08293350515340.66137540860142.981554438691.0753094462106.160960938
160.433890984785-0.424893573417-0.3206943370010.6044652986650.4125983860880.4872786872-0.6946725113491.03020695627-0.343325658763-0.01014180984330.366879065572-0.06830915146570.522279655955-0.355556058693-0.01702765979271.29702905908-0.6911732335110.05934281125731.84838311955-0.005202317013930.87440091367232.734941154981.5944678915108.662604668
170.235368620688-0.0177063930069-0.0886643634440.3147398024130.1722446218410.111089399425-0.1710479202230.3044392646560.05250505815090.219332551142-0.01393805020550.0239627645652-0.11135181461-0.05566741838092.29216870631E-50.947738125769-0.288346330717-0.009927507115941.20924982060.1660329065750.83986786888131.519288641687.7548139021128.333954072
180.0605784448610.109075886981-0.011494556920.151334670837-0.02691797042290.0335702083063-0.1302054335080.117216958535-0.04351906016040.6984205622930.0732375631211-0.5857446309210.424394359647-0.7007755974540.0001197716087651.03610007253-0.2844462944850.1990407125431.17959362368-0.140174162071.1166832207121.968911821578.1516482682157.576138611
190.110459501605-0.0544840825526-0.03432980012970.01952317349620.02368408809280.01522431146360.2137925647850.53120892019-0.053718795923-0.199292586793-0.1011588279230.4013797891680.1917518659560.171858638772-0.0001259970394411.443033008530.2173993120640.1979346681381.877506753520.02845548614761.02945909667120.37928872782.701444160483.1185614218
200.239581375345-0.262490044618-0.07797438244170.3488134848490.3184900570820.249097997030.4699119262410.1988759387630.402582487095-0.480875804302-0.6106202926790.03922110133290.4627705756090.0870758733469-0.01023553922491.01108151487-0.1150022315160.2827241109641.564705666780.1056908862010.846711940023112.72990696391.891233667586.9506905939
210.4980132303280.02723695417370.4798257064510.1652523944290.01885696633170.336727854283-0.04516058552520.5473862057590.272994592849-0.0388074451102-0.01891114521070.04654597813520.755949347750.1661203259051.85859436746E-51.131554493490.03307204042840.3206220252051.646781302410.07652709456490.760177398848117.49119647888.867754831384.126555306
22-0.01599363430680.005000823926750.03235729104130.04364648802180.05916428488730.02579991166380.005360879957780.488166429111-0.1580648253990.2578659583340.205180763163-0.3119408214890.0805936783339-0.3757923023220.0002481612175662.05356370140.7548130123230.1159334734382.660743905590.003927995123521.44808964212155.43630887685.515028435877.6219988952
230.014097848614-0.01167066460750.0388342624956-0.01716338016940.01598101579350.0102012177973-0.08146424151620.314562309591-0.3199349108110.3305920757940.378605782198-0.2767934077330.719138777818-0.198212763773-0.0001663140052451.893127487660.514829842039-0.1099190135052.215649280160.21078166941.41192376388145.58098803977.958035966281.7528305298
240.0178043707087-0.0304201178503-0.05275187519590.0108384065560.04750622258540.07595147948090.8299195166020.2458552633560.00867434328163-0.1443665850530.07803004790230.151735461870.42861693865-0.303689080693-9.93619036831E-51.550588734160.6993384528310.1258827996122.366059216870.2087515108521.39739582248152.00239442184.354562015882.7684776638
250.00554156412820.002336988383220.020463867892-0.007418266156110.001970217334290.0228055198577-0.0433657519376-0.06295574365630.1692927129770.112308611689-0.139363555284-0.4477895763090.2029359909430.2074684052920.0002290483149342.028206149681.1218717723-0.1941649210022.99568774738-0.2988054841731.81407015561150.9356118476.36694982675.5199547523
260.608816341799-0.1517535066310.4081020624750.06379419292030.06784861126630.349972260702-0.1541884255210.4014085255420.4475731817190.02197038969940.0247886941393-0.327896043720.1374471357270.399135060129-3.1657262444E-60.736230526637-0.05383348948410.1545233189031.585734830680.1214163727931.04468350088124.53005972799.6581326133102.04747539
270.02225830825440.03820272186470.008694817847150.944462049508-0.4758669402380.3035624956690.227019975790.4211281144860.156351124268-0.970686421546-0.611848120299-0.284662664071-0.007169360854850.3388017219540.1259325448181.093225995780.5276718129540.4503915766332.642498286460.5070280125111.78240967453152.7757170592.97383580584.2166756968
28-0.03479214991240.01965695985690.1295720495980.1055460162440.1808184140190.1747260371260.05516511713210.1147685357960.399900552569-0.2546406434190.0933995497559-0.546530295482-0.0887245653881.171768535887.99082367813E-51.292864454680.1398622980760.424135239312.502332822810.5023305648131.67742822581154.15898321898.788236924280.3736181057
290.1130140479750.00989410438508-0.0544769647538-0.00936584402779-0.008411988715810.0157197137247-0.30689483584-0.514676359978-0.2608592494190.5527264494920.233781675986-0.08411872931570.1532352326390.06939249082660.0001370255828631.18663424138-0.02933791683520.3492716993031.30285383260.02731386183080.94560839173215.181274350889.967206568389.4919063754
300.0368773526114-0.0280677054391-0.008948557171940.0514541452468-0.07119528939310.0640741754692-0.226541441487-0.206152118797-0.5519042613290.8923829156550.135975057204-0.7670345454680.369163087205-0.270532864710.0001734063813980.9312677950770.09410945919580.07314002093251.00675888849-0.09395014388230.77744482265325.489772464489.53660997182.4040969267
310.010178720761-0.0472276696091-0.06291960702850.2691557887970.02562686124020.201958048518-0.173036364676-0.197633893850.1725130300440.3705247447490.2039242066930.0327764731317-0.0316680577681-0.03112033043776.12408404149E-60.620726949190.02741012807050.1725726627341.03302961278-0.1122830226410.85906892471818.5405682265100.5864395480.6095634334
320.1138967949920.111593209934-0.0322809909410.113664093170.03109637434160.08503345968580.2766128057-0.709352778748-0.08202290436390.0412923247668-0.0858248932917-0.120275366788-0.1132504994010.0945162082868-1.92798116427E-50.9943988689890.1358965879110.1149075702061.1308363055-0.05107365902190.82705976518722.41661371399.081772505787.3471318076
330.489380763814-0.514850461132-0.2813008005670.320493714684-0.585443876784-0.09497215392680.140454282911-0.368000906941-0.2021454902220.1226060100460.05391423855080.0643711485845-0.1912929153920.06093504772184.74449486532E-50.7286661141010.00513095819540.2172949854991.018462108820.01304433253420.84350111765911.919682656794.165969462785.0531913206
340.0719056877873-0.0201735834811-0.04474249975090.03725708366010.05872977303220.0775552200969-0.431882338989-0.460307236523-0.6078259176150.7685255064060.02628676036131.132898822310.5970083429020.106934800134-0.00043775112970.8599360762810.03905991393910.3346629148341.17411187690.3062052142952.01881728605-20.931809593382.824700494992.8092981827
350.09052700905670.107817102908-0.065355884360.100206892641-0.07809443082390.109681280246-0.563409333184-0.694298313319-0.8738772539840.1828846579260.1307816850450.3358813308690.6125264629190.8094570078510.0109117136920.8827173531030.2697856546690.1542191721481.183243221160.2647816850922.21075750284-8.3008897452377.657160103491.6051519889
360.0119108772235-0.02119305987910.02601889020680.0630760444792-0.06339724613990.0437719040534-0.4458822697590.00838093645953-0.7617347404210.2032144381350.09488387309540.512168139624-0.291454352983-0.0968903027212-0.0001948891693680.745910850330.04196246593350.09379123164841.18494500304-0.014005813071.32660642165-8.7313053666889.880752048690.384977529
370.00970750413816-0.027622113878-0.02068716706490.02113418512740.02623808494940.11524106528-0.639681434182-0.284206535211-0.8497962488920.116845176890.321257124130.6252818169710.3543638063830.2053033439010.0002321605690660.796741041724-0.02005833801650.3747779852431.130812268340.2713593870781.84191097265-13.786815547183.670375548190.1772720188
380.00251368345784-0.0402232582493-0.0435684385296-0.003705948064160.09214599992490.0999275929866-0.226270936731-0.236241171829-1.056188927080.692901378477-0.0652027300533-0.1276406721311.204699130170.2795778972840.0006792124781161.18205314036-0.0368015936920.383518820691.32824031860.51653893672.33145029666-16.445465685475.429595928396.7442087648
390.27748823704-0.02247766367410.1612510691940.08086530537020.002834771130160.3426320423730.08060239960080.2224167368370.334023106251-0.203158357311-0.4477238818270.50150509764-0.38461650471-0.676276831131-0.03010866273260.5121536259670.03720129126260.09778546393611.07797761769-0.2090862455561.022772818155.1199162630599.438400731664.5946041354
400.4550335092370.1772065865270.1504517710680.2221849643440.2343832821510.240974993388-0.003217468713450.359252943505-0.268216923819-0.202708245437-0.2865208503140.368387094822-0.0286950752305-0.7472962224984.50230260062E-50.564334353341-0.04429803470820.1116286115391.05375707632-0.1236049246850.89690177482111.147262542492.26000132663.0534815444
410.6476582572310.3568497131690.3531551647550.333940740791-0.02153468415091.01900640940.0353001593234-0.08519493433580.00654525751144-0.119391333753-0.4065824536530.359248708953-0.31184597576-0.747830993865-0.112276392290.473934467406-0.01069263267410.1757346182031.00231366663-0.1858023119940.9108624604257.9484671443395.726516692568.367632008
420.05068616318980.0333454816645-0.06001584012680.01760862537530.0008025002916850.0240307118869-0.2382231585890.0455101166060.0150335123218-0.1529923613640.03358906180780.244917524402-0.00201346056639-0.404196109818-0.06145623952070.633276162292-0.2044460039330.2272545344971.60782962702-0.4353457794891.48738919636-12.909429129988.317881443668.3550583109
430.274350883924-0.2326292267610.1197428753290.113436988267-0.1076738532880.0391418218878-0.205647901370.10549953092-1.448339030580.2653222677790.3351723984970.5248794242340.4806758983140.393447875355-0.0003005207760740.7463479059460.03028497325920.2666524907761.243410309950.1423224902651.52168425-20.352719691189.215204652188.8386446965
440.1143719272460.03773934003860.2645961377910.278636514055-0.4557923788461.50119980954-0.253417136045-0.407036270098-1.09975709701-0.05653136756010.1832575171080.23229313039-0.4228731400950.317372406653-0.2934499889060.5494170462760.0006745358897230.2894316934031.196184166720.06690258956061.43135715464-17.441319578894.278772231383.3107375949
450.145023873929-0.221058079437-0.162743640990.3482851063580.1448599640590.162242106057-0.102823473248-0.163983281687-1.322571414540.349229886983-0.1316731442010.486280202259-0.0886817060717-0.731741944795-0.001903149349620.6251950268020.04381073365880.2548907757861.312237518940.07549606787011.35974286452-26.943058875695.242493516390.4570182456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 67 )
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 304 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 454 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 111 )
5X-RAY DIFFRACTION5chain 'B' and (resid 112 through 360 )
6X-RAY DIFFRACTION6chain 'B' and (resid 361 through 466 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 67 )
8X-RAY DIFFRACTION8chain 'C' and (resid 68 through 304 )
9X-RAY DIFFRACTION9chain 'C' and (resid 305 through 453 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 40 )
11X-RAY DIFFRACTION11chain 'D' and (resid 41 through 86 )
12X-RAY DIFFRACTION12chain 'D' and (resid 87 through 156 )
13X-RAY DIFFRACTION13chain 'D' and (resid 157 through 189 )
14X-RAY DIFFRACTION14chain 'D' and (resid 190 through 339 )
15X-RAY DIFFRACTION15chain 'D' and (resid 340 through 365 )
16X-RAY DIFFRACTION16chain 'D' and (resid 366 through 403 )
17X-RAY DIFFRACTION17chain 'D' and (resid 404 through 438 )
18X-RAY DIFFRACTION18chain 'D' and (resid 439 through 471 )
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 16 )
20X-RAY DIFFRACTION20chain 'E' and (resid 17 through 64 )
21X-RAY DIFFRACTION21chain 'E' and (resid 65 through 125 )
22X-RAY DIFFRACTION22chain 'E' and (resid 126 through 151 )
23X-RAY DIFFRACTION23chain 'E' and (resid 152 through 165 )
24X-RAY DIFFRACTION24chain 'E' and (resid 166 through 199 )
25X-RAY DIFFRACTION25chain 'E' and (resid 200 through 219 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 102 )
27X-RAY DIFFRACTION27chain 'F' and (resid 103 through 129 )
28X-RAY DIFFRACTION28chain 'F' and (resid 130 through 214 )
29X-RAY DIFFRACTION29chain 'H' and (resid 1 through 17 )
30X-RAY DIFFRACTION30chain 'H' and (resid 18 through 32 )
31X-RAY DIFFRACTION31chain 'H' and (resid 33 through 60 )
32X-RAY DIFFRACTION32chain 'H' and (resid 61 through 83 )
33X-RAY DIFFRACTION33chain 'H' and (resid 84 through 127 )
34X-RAY DIFFRACTION34chain 'H' and (resid 128 through 151 )
35X-RAY DIFFRACTION35chain 'H' and (resid 152 through 168 )
36X-RAY DIFFRACTION36chain 'H' and (resid 169 through 179 )
37X-RAY DIFFRACTION37chain 'H' and (resid 180 through 190 )
38X-RAY DIFFRACTION38chain 'H' and (resid 191 through 219 )
39X-RAY DIFFRACTION39chain 'L' and (resid 1 through 38 )
40X-RAY DIFFRACTION40chain 'L' and (resid 39 through 75 )
41X-RAY DIFFRACTION41chain 'L' and (resid 76 through 102 )
42X-RAY DIFFRACTION42chain 'L' and (resid 103 through 113 )
43X-RAY DIFFRACTION43chain 'L' and (resid 114 through 144 )
44X-RAY DIFFRACTION44chain 'L' and (resid 145 through 174 )
45X-RAY DIFFRACTION45chain 'L' and (resid 175 through 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