[English] 日本語
Yorodumi
- PDB-7u9f: Integrin alaphIIBbeta3 complex with BMS compound 4 in Mn2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u9f
TitleIntegrin alaphIIBbeta3 complex with BMS compound 4 in Mn2+
Components
  • Fab heavy chain
  • Fab light chain
  • Integrin alpha-IIb
  • Integrin beta-3
KeywordsBLOOD CLOTTING/INHIBITOR / Complex / Inhibitor / BLOOD CLOTTING / BLOOD CLOTTING-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 / 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 ...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 / 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 / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / glycinergic synapse / negative regulation of low-density lipoprotein receptor activity / angiogenesis involved in wound healing / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / 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 / Molecules associated with elastic fibres / positive regulation of leukocyte migration / positive regulation of cell-matrix adhesion / cellular response to insulin-like growth factor stimulus / smooth muscle cell migration / microvillus membrane / negative chemotaxis / cell adhesion mediated by integrin / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / activation of protein kinase activity / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / platelet-derived growth factor receptor signaling pathway / negative regulation of lipid storage / fibronectin binding / ECM proteoglycans / positive regulation of T cell migration / positive regulation of bone resorption / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / 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 / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / positive regulation of smooth muscle cell proliferation / Signaling by high-kinase activity BRAF mutants / wound healing / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet activation / platelet aggregation / ruffle membrane / VEGFA-VEGFR2 Pathway / cell-cell adhesion / 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 / regulation of protein localization
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 alpha Ig-like domain 3 / Integrin beta tail domain / 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 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 / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin alpha, N-terminal / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1.
Similarity search - Domain/homology
Chem-I7R / : / Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.70000525883 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
DepositionMar 10, 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

-
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: Fab heavy chain
F: Fab light chain
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,11241
Polymers295,7188
Non-polymers5,39433
Water19,8891104
1
A: Integrin alpha-IIb
B: Integrin beta-3
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,65020
Polymers147,8594
Non-polymers2,79016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Integrin alpha-IIb
D: Integrin beta-3
E: Fab heavy chain
F: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,46221
Polymers147,8594
Non-polymers2,60317
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)259.397, 144.292, 104.923
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 / GPalpha IIb / GPIIb / Platelet membrane glycoprotein IIb


Mass: 49228.625 Da / Num. of mol.: 2
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: 51958.789 Da / Num. of mol.: 2
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 Fab heavy chain


Mass: 23339.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Antibody Fab light chain


Mass: 23332.686 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) 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, 1131 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-I7R / (4-{[(5S)-3-{4-[(E)-imino(4-methylpiperazin-1-yl)methyl]phenyl}-4,5-dihydro-1,2-oxazol-5-yl]methyl}piperazin-1-yl)acetic acid


Mass: 428.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H32N6O3 / 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.: 1104 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.96 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 11-13% PEG 8000, 0.2 M Ammonium Sulfate, 0.1 M Tris-HCl, pH 8.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97938 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 107262 / % possible obs: 98.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 56.1740325034 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.5
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 0.995 / Num. unique obs: 6873

-
Processing

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

3nig


Resolution: 2.70000525883→46.086284695 Å / SU ML: 0.372230079298 / Cross valid method: FREE R-VALUE / σ(F): 1.33576223462 / Phase error: 25.7020469978
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237424331538 1998 1.86272864575 %
Rwork0.216574099172 105264 -
obs0.216968496148 107262 98.6888956361 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.4792081097 Å2
Refinement stepCycle: LAST / Resolution: 2.70000525883→46.086284695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20715 0 318 1104 22137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059917173286321731
X-RAY DIFFRACTIONf_angle_d0.53153547355129510
X-RAY DIFFRACTIONf_chiral_restr0.0420064291943280
X-RAY DIFFRACTIONf_plane_restr0.00358734301233818
X-RAY DIFFRACTIONf_dihedral_angle_d11.802515258612957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.70000525883-2.76750.3642220538381330.338906217466899X-RAY DIFFRACTION91.9335860897
2.7675-2.84230.3470048757421360.320150946097315X-RAY DIFFRACTION97.2461498303
2.8423-2.9260.318819334691430.3090208440957514X-RAY DIFFRACTION99.4286456304
2.926-3.02040.3269854138481420.2984482383427499X-RAY DIFFRACTION99.5699765442
3.0204-3.12830.3127973874621430.2800696164867510X-RAY DIFFRACTION99.5836044242
3.1283-3.25350.2709911681511430.257457923597522X-RAY DIFFRACTION99.6878657823
3.2535-3.40160.2542394798521440.2424112139297566X-RAY DIFFRACTION99.7154681842
3.4016-3.58080.2495326151771430.220354546497557X-RAY DIFFRACTION99.7926386729
3.5808-3.80510.2193426551241440.2108393694097592X-RAY DIFFRACTION99.7678617488
3.8051-4.09870.2204843784781430.199768811287546X-RAY DIFFRACTION99.4695989651
4.0987-4.51090.1869645829861440.1836063470067600X-RAY DIFFRACTION99.1422353092
4.5109-5.16280.2218128489711460.1744133693737629X-RAY DIFFRACTION99.4754350051
5.1628-6.50170.1895137186641450.196566804317695X-RAY DIFFRACTION99.3033565548
6.5017-46.0862846950.218197015421490.1854264760587820X-RAY DIFFRACTION97.503976508
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.75713001297-0.09202030443460.0480766316031.60445812861-0.08718698756621.515587577270.1484204234380.2155938508290.0459585635007-0.381510915778-0.1244855127010.341422243522-0.124716039593-0.302828601329-6.34718635775E-50.4522142852730.0489488549580.08554248653170.3230189557390.06392498048530.45957238089746.994323576790.143157155238.9126942694
21.27811226002-0.0754382298887-0.3153562972511.46541953310.1925568501971.089391037480.107889129883-0.1203050014320.05168062034040.343308002735-0.1575593697620.3013919258830.120864870789-0.24322592908-0.003748899882120.508466087735-0.03716836797560.1606511054920.251641121248-0.002318126007120.49984189100244.603852425492.907456627662.0996762088
31.511768656460.4692578283280.1011890465452.706901711370.3977121768172.485810698530.03430861695850.00136457112759-0.1322166729180.159863257386-0.00198265446283-0.1733480097710.2504851234950.1587018997690.004412962884330.4008609040820.08866794083940.0942914976420.2028013176430.04470133821420.39145337212664.53865859283.463063511247.7747439375
40.0296301095579-0.0770588701246-0.04912709673460.2932797129510.1197036627320.0634054859703-0.3756357297320.736744246209-0.7607345305750.3613962018510.198303473016-0.8508622183940.4423191252061.67106942890.02066426644840.9751951293370.6693188909650.1160276678812.34073253941-0.2573745469471.46429638475122.93643479986.010414726234.7865855789
51.061620605180.3857885372660.4062986659540.574438386631-0.3248129109470.9832662356240.1088089842190.1844712749520.4414643513950.01479178667220.339819443628-0.593466106189-0.1524672530951.334965192060.0002879771035220.657654330679-0.02364685488390.01082980302871.35331272987-0.07476343801651.07545950055107.088541156110.22718756849.2892298033
61.528592696280.7427730727670.08761872917982.626598057220.6715545948151.409581241330.129297942366-0.09863048968150.2153408061990.249067085578-0.0937534131475-0.00576799327492-0.233952181550.116942682115-0.003654215317280.515689088725-0.005888512109980.09053496344720.1837833127390.01673507270230.44175124872267.05769139117.40559041563.6367542064
70.774549034473-0.401992461088-0.7855002443160.480368509203-0.08830355461850.839556906085-0.1120116227730.025966261637-0.2988541570320.2247431143780.0286762122169-0.1890830076850.6490633824820.907563741158-0.006208814454330.7238602860110.115496733932-0.1094858184530.921030012562-0.08528489830410.92568506827996.0949488477106.40774797962.1288141407
80.283845856564-0.0629872647490.2237787906080.143987397012-0.2494923020380.4355627003530.3222738380040.347540822128-0.0959138399697-0.387702633951-0.45601892192-0.147143798901-0.09136328899290.289399934234-3.84976668887E-50.6215511299940.121821921791-0.05686338468611.02403613914-0.08520934548260.99335199409899.0390905472103.93403126744.3812386956
90.102878481744-0.03428879145910.02728533479270.0631043194868-0.01906153041030.0593871410159-0.0530238737870.0841377429440.311788411556-0.2099683965590.437734118883-0.6042341378170.05452916986660.2686824101210.0002261324835361.048197272950.2762626199930.2248958971992.293489178690.03856339003961.21568275727115.59950919688.768233732719.3744425603
102.242550056170.0501757990241-0.4774718283981.457449855620.7169009767751.41523410513-0.241366339836-0.2171456424530.0919841726785-0.108608394407-0.0391753446921-0.266814929020.2546364631970.747747517534-9.01907406698E-50.4421348735770.04112536207740.04525525164530.6999827403370.06428181515790.5095384429487.429551454694.047243868132.007835362
113.019329657090.405064883154-0.3330266371450.92129802663-0.9689553170411.59334856914-0.4331143392370.872297263187-0.131954122309-0.3566941277080.115090860147-0.2930359299450.3999201116350.5731003471650.01403973136480.647695671809-0.07087347215310.2022441534390.927186804185-0.0108318376410.55409391449291.413371523989.3757615086108.288667958
123.321781984370.08308534339050.4443308909522.338537077210.04291323001243.10370550325-0.4103323647550.184762679906-0.542692335429-0.1578032934890.174002201848-0.1404136638440.6970724125480.155418285974-0.02196598666850.637715569924-0.005007206218520.252465599240.415827133806-0.01282498366650.51763542612173.51773285579.3035029227126.04908813
131.39699919878-0.15001346387-0.2935703688920.3668551462970.6582104382831.42629620906-0.3854691418980.5931735883820.0110994635-0.03129245578160.2927767505120.3499698483010.596968502891-1.32807434953-0.00244499316410.846986877207-0.4250448501820.01484344763211.384797418890.1073060293490.87513578741221.16589491981.6965847085128.212859958
142.51085451555-0.3827906484710.8849402102571.07472024984-0.584547563212.57709059174-0.2589990338740.9145796398330.536106411655-0.3028754631920.1554246421140.0795992844354-0.151377475248-0.222214548725-0.07022793113230.628341833102-0.286147764417-0.04929691321720.9512513015690.2633171775730.54097800397661.6036484374102.983072794100.417710117
150.309630280553-0.10989369759-0.6650628151250.04077342500610.2641239347510.825131147742-0.6407424021720.916703777979-0.378681470711-0.1664397966210.348439855910.02984183315541.01247655092-0.444134422101-0.0253762257671.00817714255-0.596333320387-0.003265039487021.527070852680.09402730141990.701885338737.04096218885.7426407731107.614816438
160.58529816363-0.282833911949-0.1753135436980.4309238861850.3269967061980.326745629638-0.3170950107490.148111451233-0.06318114500430.1134854100570.04137061174190.0839802192948-0.2513657443530.023478692887-4.98203976934E-50.798691092544-0.191462808458-0.02748263775910.9834393854030.1326937886910.70203497766933.464762842388.8911668405125.519421138
170.3474243305240.3137829104630.08423723908620.3257261264240.1666958850830.144527979408-0.464768565855-0.124882626092-0.03253440556130.409121212992-0.02470672800930.1305684693570.0644709245164-1.236073262570.0001435814351921.19455939765-0.2808419649570.2074016628911.16000067084-0.1180550565781.060026010621.886721924378.5634000876155.261480545
181.0825584076-0.6305969432970.1092483158510.861551036960.4490349734020.5053522292150.1852545925680.82524025853-0.0137415010721-0.396950826745-0.239225461449-0.0843059515860.594345380348-0.05234105215630.0001973435196171.01886887568-0.1069356334510.2202788627731.863523314890.07281561019890.827482662101115.99286840789.102814182385.0697393338
190.003668661385710.007983310169980.0267954944610.0147739450090.001797304681450.04432093211980.2233811270530.5469562371650.09203170015030.2781274364910.306039206782-1.11161996496-0.0419042933898-0.2818483046730.0002810714533022.199952873831.01959910743-0.06184638624763.19228815667-0.2044097102471.55096505278157.58594617686.093478115978.9963876137
20-0.000718174941869-0.003347596883390.001477724227110.02648533575330.02561565795210.01132060449040.1053357395260.190261894752-0.4228568012630.0158029778924-0.348336756711-0.701091821153-0.1149149983510.017705980426-0.0004676456706481.804349890050.3853337485480.07385923982962.117975130050.1889001473591.39154384321144.2071605778.28742666280.9780051827
210.04163241680870.0431527679263-0.00847111403520.0442264533127-0.007052447249310.004600889771890.644772808860.0866119590519-0.1491676681-0.393978174562-0.02361654496050.305075457194-0.209565188545-0.144822657579-0.0002207537448141.240267275630.3638987085860.1154742689242.674726586570.2808591560941.43658322587143.58402155987.494476279880.3584140677
220.256234293964-0.08798870358490.05853199851520.191966675665-0.1140232122330.2005079604970.4512248803060.0483227415131-0.1700590752370.09054021327680.2617654739380.1005138494840.340728734208-0.08754118693310.07004688323661.813575694661.50508319043-0.1755953400762.603517618020.1370889904051.28883822872162.98309437979.640838025586.5749586078
23-0.001337541552640.0288465065763-0.007129232714490.0226409233053-0.02355593496420.01597166395950.0927029090036-0.03177119908440.182202980333-0.1223240314220.0786175203438-0.7996309346230.06008229261240.171704916814-0.0001761980942451.664634694820.939237983721-0.4540336097832.41482352552-0.5417361641391.57323255094150.55518937776.211793392775.7135757922
240.478816894502-0.1075075107750.2457763381320.2745669872790.03504784552730.662406256336-0.1243648561530.278742224150.4780275393080.0794969038888-0.0544227451782-0.387611250320.0302627148040.820527588743-0.004678738691190.624313289344-0.1125141854740.114866699981.786559910840.1436064080091.01665658305126.38998745399.4627675384101.842420244
250.1042555795120.08031066250370.1291224191740.448205927154-0.1744965562030.3535541220320.101635246980.306773337637-0.0978932639691-0.6571959452280.01781217220820.02024653205460.166224681043-0.02590034416350.1607985531331.706657393740.9319668141460.6329815447543.463643460090.193089935611.22986936756156.59512893888.962671761772.4856809011
260.0447426312994-0.01398468341430.01223179838140.0404454110679-0.02245409364980.01381297111680.1950529095710.68983602139-0.0536126406126-0.50696187231-0.465609190177-0.4295130393610.05136767247730.568242841982-0.0003408352300551.089946356530.2025382854770.2334026074252.848056318760.3484847586821.24482791366150.96104969896.344166140387.1209044149
27-0.01199764680540.009138462683750.05560437083720.07386989275430.1191236363030.1191757552840.09664090131510.5219962693030.0106234341677-0.534963273537-0.153369077023-0.39743470254-0.263404618920.3184094506724.27380163902E-51.252753551460.08105898381420.4461975147122.442603938010.473982150551.43823145196151.91360822598.640495330977.974913305
28-0.0208697209663-0.0370995926069-0.00392860659986-0.02678396870940.0191226737693-0.003250960202470.05341634558010.808843385192-0.00126980250692-0.311021068146-0.110001210183-0.2548117721810.3623129858670.4627497770920.0002223390745080.986276082590.05421185546070.3091005122622.441689750280.1332199387111.67832361317161.476792202100.26861328181.3355725248
290.3648748457250.0489803675270.1194367455390.133346117453-0.1412577897020.184482806036-0.303022726525-0.64467389902-0.2705068098930.7258636414590.5341397379780.06080620876830.0614638406683-0.196122969378-5.82936534173E-51.127045467690.02215201111840.3661815775971.063574784250.08389376857750.8648846247115.203708257389.640111511389.4490530534
301.031728919330.1852416385390.02485909832191.43620525984-0.8079642603381.30819045704-0.115834217271-0.486238332257-0.07716483363280.6465960634470.1522624141580.02073469175740.241668394389-0.0687073075497-2.89147657719E-50.6819095090640.0552181847740.1765633582070.803597722128-0.05553796109150.75586398432318.089312793896.185709361583.6979938959
310.0792596575156-0.0687789401114-0.1004649191190.1348505373890.0594634268550.129729117217-0.0921474746923-0.273463588277-0.726203510556-0.0399109656811-0.4100169938030.9691032391770.8817372738760.281534163022-0.005404738889140.7750513300870.03908041845060.1924679800161.140026944560.4115165853962.08221496742-20.300103526982.75210562393.2979172909
320.1630224366050.348839053629-0.2222247157540.764910449075-0.5963656139391.50827022824-0.562735572226-0.443592897674-1.17547540646-0.1608908890560.003134817943660.5925449058950.9700575039370.0981541214074-0.08483298509560.7823494498330.2312857032510.2813139546211.061910481140.1208999651162.39254173457-8.3520606683877.399472864491.4901786124
330.0393917089388-0.04379357150710.1054071216630.1242909748-0.05491541149680.223819724809-0.648830554423-0.401525286603-0.7608473917750.4994559983840.3547227225220.479598052264-0.176349394131-0.378613903989-0.0009182908937210.6688921789830.1244421714360.1141716464631.128881992830.04954698179771.49767393159-8.7334949222989.658728295290.2315326448
340.1708012849-0.09996685945780.1885501649690.191435097144-0.2168930554280.325407905707-0.426041789060.247109196108-1.13070702732-0.07374739975540.2790941165120.7229397509470.641053959261-0.316317891474-0.1898600602290.300589976312-0.244211429880.5421465823911.205124970050.4724650945292.08144290951-13.845500248583.461808367690.0350636134
350.01591220322020.00546258276668-0.02256337171130.007388656957580.00715637151060.0500032355936-0.322330533751-0.0416036421581-0.4808140651450.30841797535-0.01299133380870.6138784826410.7724905578950.2137578307720.0001706169343671.11091346532-0.06171080058390.2389263029551.237244131620.3093542209922.53061952157-19.187945607973.041295919393.0869381658
360.00747885693514-0.0154541597662-1.13219281095E-50.02085355026830.0264702522818-0.01159074410320.186669665281-0.1177594846060.1828750391160.0575363509945-0.163495226089-0.4296020324240.6707559575450.2027985468190.0001068179405740.7839179048-0.009597990307190.1461520904731.067482910680.6537848343051.78986901823-13.752194048477.4480683187100.248717596
371.17537724747-0.08554879745420.1851283556790.5134055093550.5395617314190.5678762845480.03711590866440.3209971807-0.106685688916-0.195118838831-0.3205018536420.621914485675-0.140522342357-0.816189656071-0.002373615163350.4901261654560.03309162158830.08790701690140.894064174973-0.1909917878720.9677802150858.1877999124295.724281870763.8682962172
380.271748139059-0.0659471653395-0.2039960211470.266552007130.01510644361690.525237469333-0.1754229207040.0744200840166-0.518906129106-0.690676345878-0.1642701184130.454746821521-0.15812946869-0.764226894456-0.008660821971450.407207221983-0.003002585096580.1655683887380.842676718615-0.1569092041581.012638322538.0450533864695.494545569268.4126826773
390.0288494579270.0477550844085-0.05111770627380.0717884578131-0.0529452242270.0550920241342-0.07549594234760.0913888395324-0.0585308894294-0.1665051023220.1098717973670.2789800959280.124108766383-0.471671534271-0.0397058033125-0.30797085277-0.2829812617940.2260370600161.81335240776-0.9081650120111.78530445975-12.849143133588.217855671668.2935125855
400.45719712497-0.6855105039740.03889230500581.802233364230.6912372858160.705263316642-0.397345959436-0.72168325252-1.260934861231.039422342650.6658037023520.2630285909630.3434086353980.05097400436270.04887707970850.7737862559070.0740903107690.4551087487981.12284781540.484031990241.87012119637-22.836003930787.504293329397.0774166993
410.146543740976-0.0867886234282-0.1137472677010.811549902086-0.02861925107080.1511837605350.0225178076960.325691921802-1.338641351250.178947561310.1102353564460.3320615063320.2243346397670.1944954241120.3363070997460.3570616495540.02016103360730.2798522455441.22922343576-0.07147800640621.71419762403-18.199164026790.439176362881.4416129599
420.40012934202-0.03563533815730.6587041715741.04395925914-0.6307709178431.75606029595-0.425852494486-0.555042139504-1.262971740890.4492265506920.2826594416440.15797329786-0.8370280962210.209570878634-0.2364421073720.3109074986010.07110745326340.3711385194561.11657267410.2478852820341.52003377084-18.971451849194.991793027988.0070525482
430.1243216393640.04118492981520.07821935800440.4233757691770.2535251078710.168585923211-0.0699513722730.32497197031-1.550767616730.249979063017-0.2994773995970.8347405626830.184670963154-1.29922701094-0.002897538287390.608099472547-0.02765154717410.2697783284491.35578205818-0.08870911000411.52974732198-29.459080384194.229637842986.0770037498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 304 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 454 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 47 )
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 111 )
6X-RAY DIFFRACTION6chain 'B' and (resid 112 through 339 )
7X-RAY DIFFRACTION7chain 'B' and (resid 340 through 403 )
8X-RAY DIFFRACTION8chain 'B' and (resid 404 through 431 )
9X-RAY DIFFRACTION9chain 'B' and (resid 432 through 466 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 61 )
11X-RAY DIFFRACTION11chain 'C' and (resid 62 through 281 )
12X-RAY DIFFRACTION12chain 'C' and (resid 282 through 453 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 111 )
14X-RAY DIFFRACTION14chain 'D' and (resid 112 through 339 )
15X-RAY DIFFRACTION15chain 'D' and (resid 340 through 403 )
16X-RAY DIFFRACTION16chain 'D' and (resid 404 through 432 )
17X-RAY DIFFRACTION17chain 'D' and (resid 433 through 471 )
18X-RAY DIFFRACTION18chain 'E' and (resid 1 through 127 )
19X-RAY DIFFRACTION19chain 'E' and (resid 128 through 149 )
20X-RAY DIFFRACTION20chain 'E' and (resid 150 through 165 )
21X-RAY DIFFRACTION21chain 'E' and (resid 166 through 185 )
22X-RAY DIFFRACTION22chain 'E' and (resid 186 through 199 )
23X-RAY DIFFRACTION23chain 'E' and (resid 200 through 219 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 113 )
25X-RAY DIFFRACTION25chain 'F' and (resid 114 through 129 )
26X-RAY DIFFRACTION26chain 'F' and (resid 130 through 144 )
27X-RAY DIFFRACTION27chain 'F' and (resid 145 through 197 )
28X-RAY DIFFRACTION28chain 'F' and (resid 198 through 214 )
29X-RAY DIFFRACTION29chain 'H' and (resid 1 through 17 )
30X-RAY DIFFRACTION30chain 'H' and (resid 18 through 125 )
31X-RAY DIFFRACTION31chain 'H' and (resid 126 through 151 )
32X-RAY DIFFRACTION32chain 'H' and (resid 152 through 168 )
33X-RAY DIFFRACTION33chain 'H' and (resid 169 through 179 )
34X-RAY DIFFRACTION34chain 'H' and (resid 180 through 190 )
35X-RAY DIFFRACTION35chain 'H' and (resid 191 through 205 )
36X-RAY DIFFRACTION36chain 'H' and (resid 206 through 219 )
37X-RAY DIFFRACTION37chain 'L' and (resid 1 through 75 )
38X-RAY DIFFRACTION38chain 'L' and (resid 76 through 102 )
39X-RAY DIFFRACTION39chain 'L' and (resid 103 through 113 )
40X-RAY DIFFRACTION40chain 'L' and (resid 114 through 128 )
41X-RAY DIFFRACTION41chain 'L' and (resid 129 through 144 )
42X-RAY DIFFRACTION42chain 'L' and (resid 145 through 188 )
43X-RAY DIFFRACTION43chain 'L' and (resid 189 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://pdbjlvh1.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