[English] 日本語
Yorodumi
- PDB-7udg: Integrin alaphIIBbeta3 complex with lotrafiban -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7udg
TitleIntegrin alaphIIBbeta3 complex with lotrafiban
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 / 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 ...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 / maintenance of postsynaptic specialization structure / 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 / glycinergic synapse / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / negative regulation of low-density lipoprotein receptor activity / angiogenesis involved in wound healing / Elastic fibre formation / cell-substrate junction assembly / mesodermal cell differentiation / regulation of release of sequestered calcium ion into cytosol / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / positive regulation of fibroblast migration / extracellular matrix binding / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of cell adhesion mediated by integrin / 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 / cell adhesion mediated by integrin / Syndecan interactions / negative chemotaxis / p130Cas linkage to MAPK signaling for integrins / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / activation of protein kinase activity / 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 / negative regulation of lipid storage / platelet-derived growth factor receptor signaling pathway / fibronectin binding / ECM proteoglycans / positive regulation of bone resorption / positive regulation of T cell migration / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / embryo implantation / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / positive regulation of endothelial cell migration / response to activity / protein kinase C binding / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / wound healing / platelet activation / cell-cell adhesion / platelet aggregation / ruffle membrane / VEGFA-VEGFR2 Pathway / 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 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 2. / EGF-like domain signature 1.
Similarity search - Domain/homology
Lotrafiban / Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.80006901797 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 19, 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 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)302,63440
Polymers297,4068
Non-polymers5,22832
Water12,394688
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)151,39319
Polymers148,7034
Non-polymers2,69015
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)151,24121
Polymers148,7034
Non-polymers2,53817
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)256.760, 144.170, 104.550
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 / N-Acetylglucosamine


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, 714 molecules

#8: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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.: 10 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#12: Chemical ChemComp-MWI / Lotrafiban / [(2S)-7-([4,4'-bipiperidine]-1-carbonyl)-4-methyl-3-oxo-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-2-yl]acetic acid


Mass: 428.525 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H32N4O4 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 11% PEG 8000, 0.2 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.996 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.996 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 183986 / % possible obs: 99.6 % / Redundancy: 5 % / Biso Wilson estimate: 73.7470023912 Å2 / CC1/2: 0.983 / Net I/σ(I): 4.66
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 13682 / CC1/2: 0.141

-
Processing

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

3t3p


Resolution: 2.80006901797→49.1441518768 Å / SU ML: 0.501160464347 / Cross valid method: FREE R-VALUE / σ(F): 1.12852072606 / Phase error: 27.9506718708
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234941078932 3805 2.06860932913 %
Rwork0.212865903006 180135 -
obs0.213321122371 183940 99.6165677397 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.318110988 Å2
Refinement stepCycle: LAST / Resolution: 2.80006901797→49.1441518768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20715 0 317 688 21720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006193923501421709
X-RAY DIFFRACTIONf_angle_d0.60495621996829498
X-RAY DIFFRACTIONf_chiral_restr0.04381798357363281
X-RAY DIFFRACTIONf_plane_restr0.003941724613013815
X-RAY DIFFRACTIONf_dihedral_angle_d11.671545648612915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.83550.3854211083881410.3998409658976750X-RAY DIFFRACTION99.5809248555
2.8355-2.87280.4108774582631360.3828849801926652X-RAY DIFFRACTION99.7355274758
2.8728-2.91220.3948928103831430.3774710981466668X-RAY DIFFRACTION99.6488661302
2.9122-2.95380.3382332989941440.3644072244256647X-RAY DIFFRACTION99.5018315018
2.9538-2.99780.3883138950061370.3632368670866673X-RAY DIFFRACTION99.6050899517
2.9978-3.04470.3679076119831380.3556913299196631X-RAY DIFFRACTION99.6173657101
3.0447-3.09460.3609097424031410.3509197063896749X-RAY DIFFRACTION99.6240601504
3.0946-3.14790.3170537876991400.3248135161726626X-RAY DIFFRACTION99.6025320183
3.1479-3.20520.3415238595151420.3099588900936681X-RAY DIFFRACTION99.5913005401
3.2052-3.26680.3282792460031450.2950444658156672X-RAY DIFFRACTION99.7512437811
3.2668-3.33350.3494449842521400.2827685083996661X-RAY DIFFRACTION99.444363211
3.3335-3.40590.3052246773611360.270353396526684X-RAY DIFFRACTION99.736765136
3.4059-3.48520.2557486417261430.248864592876685X-RAY DIFFRACTION99.5480390728
3.4852-3.57230.2501969372921420.2428235874416658X-RAY DIFFRACTION99.6191034281
3.5723-3.66880.2546995914771400.2366794513596614X-RAY DIFFRACTION99.469808542
3.6688-3.77680.241474195811420.2198606616796736X-RAY DIFFRACTION99.6956080591
3.7768-3.89860.2335333716781430.2094025900956653X-RAY DIFFRACTION99.6042796424
3.8986-4.03790.2008589522931390.1909011298916662X-RAY DIFFRACTION99.6337532962
4.0379-4.19950.1878785193181400.1850031986296647X-RAY DIFFRACTION99.6330005872
4.1995-4.39050.1994818612131430.1683503139866696X-RAY DIFFRACTION99.5487627365
4.3905-4.62180.1867109998691430.1579939855146652X-RAY DIFFRACTION99.7797356828
4.6218-4.91110.1670423963361400.1599659479796647X-RAY DIFFRACTION99.6330005872
4.9111-5.28990.2005754574941430.157465936566724X-RAY DIFFRACTION99.6517196343
5.2899-5.82150.1921892875871420.1734124784596641X-RAY DIFFRACTION99.6913580247
5.8215-6.66210.2065993094841370.1860699759066708X-RAY DIFFRACTION99.7377240274
6.6621-8.38680.1997214911811440.1730651172746653X-RAY DIFFRACTION99.6773720487
8.3868-49.14415187680.195070874771410.16205689026665X-RAY DIFFRACTION99.3431615823
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)
16.92616771254-2.2328391209-2.166311596565.889648841331.938559120096.222239739160.0722427725960.3691245129320.188691712051-0.515735970171-0.07393392442470.191064727726-0.109861706791-0.368909810442-0.0238112447550.4949837458230.0128313727369-0.03073193304330.3637725267450.09068692093190.41150614720146.519661753589.873713231838.5645518541
21.9798466682-0.0252723719879-0.6878221268872.789734325520.6265761905132.539812229490.164072769013-0.04563613694780.1272751821520.350085252007-0.2258286901260.3977457905420.0465981331545-0.3379539937660.08150099424940.576256583183-0.01343984802980.1247495109360.4815148320070.008319538870390.65802295337437.45502524797.196170845559.1707241606
32.61267827011-0.816905603341-0.5332227983472.613914066340.5456909082111.914197231370.0151013485788-0.406427350185-0.2474699658110.701547490892-0.0654081056440.3195745164820.7115228597-0.24077302284-0.01182584824890.838731995466-0.02232625746440.07948923486680.4371136967470.09065247945540.51555963415955.146961178685.493076244965.9803220711
44.579431426622.97080111034-1.146711043028.17623334087-1.518386547055.171997108990.0722415284872-0.243525341026-0.4561870086960.585748387533-0.0730218237687-0.6935885297020.2454282111130.3694609100190.02928959154140.5810658488620.1422764208130.01289621182930.4241773611470.05345022434510.46169845489369.69907820486.13950458157.0347909539
52.754769126650.612329938373-0.3195077736793.6710490150.6444605918893.15661130370.0429018691959-0.149044785293-0.3810300861040.4903936251390.00484448879773-0.3357430771020.7845756650650.00467042154836-0.1700577241530.6077085973770.08316397552190.002748126647390.3760897628190.02538923434770.46352463284963.24501275781.180482128244.5814887887
63.19153255044-0.3356016345771.308196026723.62239182415-0.1714925463244.08427440898-0.01726975318420.138664212855-0.3304527601850.112329196508-0.00726568931262-0.1549106356090.2963554407240.02400415447310.01471580339590.5289315871040.02956946137440.08412952203380.3873678220080.0153787797780.44984881038759.16407309282.04043338340.3656118711
78.33594034126-3.40829490453-3.605094256324.659033192171.819744811554.6120222059-0.2406509685520.332919729023-0.4490867850880.4508646096580.241604206201-1.182352516350.5884093175911.860354286760.03770407896220.8413737132750.246670044595-0.09504411958681.9889738592-0.164309644981.32318683076121.46131928890.436823885335.852507923
86.75551400447-2.79574955237-4.393443711617.07163952675.687963576227.843391249620.187319778722-0.3130690247881.345989181820.4217347677420.777895916496-1.33581332267-0.284907621651.26502076785-0.9300732881770.667921178656-0.0906868891018-0.09894360673711.0740111598-0.09968391240131.06356363268101.595126775113.90039879353.4289468874
92.849690041070.791778060560.5571361889752.607091478160.4793600132441.45029136120.0416605283597-0.233127923840.3338281856730.198633767581-0.0453230351351-0.00363385069244-0.2163350126970.0350335615919-0.01581183790150.6323425188440.01030477854470.06714793945380.3464042276310.0140377646030.52296835324466.2514299284117.27332215163.0869675349
105.41954625701-3.78636865517-6.355689330384.046313164374.11257004417.51964013831-0.332477605974-0.412498349452-0.07447981532280.4205113396260.241140534376-0.3247698261230.5490959711071.086028586550.1166218091740.7509063295720.118300085934-0.1725513947021.00802127528-0.09915042660770.91520874815396.285542596105.6847357256.4488936198
118.006216908453.478702524711.390322339126.2537280271-2.8641987512.86183538037-0.2378665685270.241698571676-0.435511271543-1.372932197060.44278171552-1.421409506390.3426806264882.340690213430.08718051682771.076210788180.2445018154370.2883545465842.08725006674-0.1095402464731.19138550377115.26623762389.008418479219.4112099079
127.896820445961.2561261004-4.268154146626.04011699297-0.9053841633847.06010019991-0.258191203199-0.204293840754-0.03644740034520.09673429317470.0822277944824-0.4869516380470.1332547729510.9206750818390.1767691947550.582079423124-0.00550874779363-0.003349588659330.743385761059-0.03997542749880.4895189924786.840386792794.0398852732131.570059892
132.523973336670.507128668279-0.2491360353151.17321939099-0.8284820030612.05680422315-0.3003340353930.660431216058-0.206418986141-0.4714769566950.0536404551555-0.2893550975490.4755429682520.4598206457040.2157243920830.8147143154340.006589431664210.2231119143310.901423117031-0.0755955880260.62193061868788.429680552687.4902973385109.163360743
143.838317535340.2779298871280.8466964030093.426401664880.4002898239045.0457548819-0.3553756165730.065663233375-0.644905290508-0.145055261240.169696927872-0.05114721206320.8052832850570.01756084727840.08253072115510.6575407413330.01541265245250.175919914320.478380560958-0.0006433354282740.49200127013173.470137466679.8495740152128.029561121
152.871156513391.32616881252-2.125684538321.4862521966-1.36511519374.0355495575-0.4396943504250.9552208355550.144532895151-0.3239424911210.4605860655030.4435094888440.463671490026-1.28408250518-0.09328197913080.992843264086-0.367908165201-0.08627034602611.491039073520.05566567258190.89394876215730.633710077888.1739477682116.7899741
165.148882777380.8741765441110.3404323522964.33346410793-1.854617330243.6997784918-0.7125975939881.075667408760.405017965973-1.604515789720.412432646791-0.518427507118-0.00924045022430.05558053704670.5231549028461.11750175725-0.3088237714150.008082119179291.31749289190.3012367931880.7949119527478.0814182824107.67795018996.6912125715
174.05387920264-0.5342840085761.366435295721.60050850832-0.1367332323583.79652570842-0.1927938052120.7129353027860.340161720991-0.5438108433690.218249405660.118162060869-0.111016774731-0.620398248025-0.06241659505730.786210558922-0.184648582157-0.02421504253740.9868490072570.1772405403980.52375490998359.8851834499100.365135483103.0256777
186.064622869012.72420585841-5.975893721522.56163535535-2.972060141815.87331027311-0.3119950317870.977115119883-0.2000885638-0.3933859833940.416957122740.03774837243670.494634296591-0.753971776925-0.004603850202791.01778175011-0.304754092233-0.151188271541.527102215130.00334818084230.78584202583642.759990236390.2881692965105.542884333
194.681172551711.20402672805-2.801645620554.95674852499-0.4529805951149.12663063589-0.562203741180.888641328649-0.31328286578-0.308383171507-0.03254882023980.06492495037580.509544512753-0.4747542652260.6542719463230.886927855898-0.321699934449-0.09276642794181.172979389050.06953653911850.80298009622831.868446525683.9323512584117.713894127
207.543713200456.117738564495.925216818155.02454329474.810199804724.65616530829-0.235592555887-0.23185824544-1.382778438111.01595356583-0.2167408527020.4857598923990.928036674949-1.475491794050.6980905073351.38495486867-0.1549550355730.2738046312761.32796356274-0.09436766365911.3113312890121.416828986777.7034819223156.77268909
214.43358958224-2.786915672131.254611258534.523764737650.9475745693917.723257909240.4381840671920.4296446611540.220922830959-0.761636746517-0.231407566317-0.07313132928921.08387776516-0.308300457343-0.2167886748111.18667233875-0.1633359183810.381978259141.45025301914-0.005954516199540.903756038089113.57927302789.729511212185.8023336819
226.90455368967-2.43442803822-4.101611917092.121722175511.392543524223.29837161830.3842756765140.9784923928150.215485432082-0.376766420677-0.236048795134-0.3983239467050.763165668766-0.2687932781560.01237971293941.31359889108-0.08755499431150.3033648940281.57733104434-0.003644200033710.903989040994117.45374854688.591191689983.4552816946
234.848680053013.23477101032-0.06378482939027.451122126724.851510604144.517276964990.6302177688561.69485773525-0.196674217924-0.2709901439280.585295257778-2.70289409020.5812262299941.21871951163-1.071415622711.634484190560.7804129583820.2258393164892.971249784990.2812595027532.18534286764157.09040560686.589655617978.450080626
246.344611930732.71772471439-0.2471113589647.506668275814.703083410794.57717058261.129896877690.6739520082570.224469154884-0.696933679877-0.593606105308-0.688798158010.253980541097-0.0425426733956-0.2021997088781.519957684710.5322594473190.1521275724132.025930264720.288655061691.2804904933143.39828223683.415145666380.1619475071
250.1012226323140.3053408115860.5498835062294.352415092561.146983350433.893884847460.8256062758581.5738849117-0.490100872699-0.376486270963-0.680472236634-0.5158712557461.017405163531.59926603922-0.6474631534611.761988057920.8735743657930.1038857140913.23571871461-0.02586815652561.96581576782159.08854056181.627209361984.5687647501
260.684353843023-1.0304442971-1.335905602841.832111967792.063858560422.773796435110.4375027298331.19098315518-0.31012422713-0.538404989094-0.541850066898-0.4590073723650.09067744607510.7014694143880.008230771719091.747644507010.971895038205-0.2617896061543.10036079142-0.351066789341.84042843176150.15261043476.669866068875.1788520678
274.23786728524-1.591655076981.833639753162.2546653236-0.2767180380342.03533668068-0.1892511824540.3383122954420.729356700072-0.2657467423550.0137077397561-0.7534582963570.02781074883940.7085494592280.1229412049680.853281156158-0.1690343016190.2405631230631.438173892550.02552590806481.21226602545123.55415756199.6893803036101.613452084
285.785316003760.956316038152-2.523480501531.07544848550.5431049189372.09632189574-0.134010719779-0.572096829885-0.129631609231-0.773020555737-0.219609544037-0.674458204120.2744871113312.299701341670.7424915489251.54996586070.2669449747350.5785818910592.556922172920.6820292143361.81036280791151.754271497.12462393682.7106468533
295.944525672191.37421831861-3.375632997010.843488556790.6117773871688.26849913676-0.2630738374680.4839310062460.00288644988871-0.9802403111820.174626339371-0.669060779791-0.3536811948421.380283885470.2430681706791.38002426611-0.008808304014140.5001648560562.211490379130.4552972881721.79535473087153.57796169498.204594590179.0553946078
307.14001808852-3.89366799604-4.683700647673.354804114324.996422164168.29495561426-1.26802610502-1.53213511677-0.490524666561.830045183590.735314270430.5723101652881.576018249030.02664744185870.2230727359151.39494257710.03656165116220.3494704246681.184882457620.09654033813650.93427888017314.950604770189.651608745988.9026504057
318.02154599787-5.14289749958-5.280218286337.950277349845.193191460584.23001456667-0.463320926999-1.45799539107-0.4659037071151.490539323720.276540612116-0.4624758749871.79010845530.628911260815-0.2595324470611.09708451102-0.0326100011652-0.03237796059421.10137273684-0.003634341265330.86022101822825.223172098889.195301976681.846099326
325.177306718521.589264682691.807790865136.08448132064-0.1443905646117.88296872298-0.0924951876385-1.004789727990.1420408150810.8106043044030.05890994818470.280789731745-0.4021486456860.0193316288979-0.05294895842210.6606623868380.03899446680490.1923498604810.898043863602-0.07314644531970.57514219458919.804126169699.640384968682.8688562018
336.523581464510.169862602693-4.303624475981.91990574049-1.69889757985.171637716380.0154926780772-0.675333725446-0.01043870262590.5062002767690.2039381045310.409791690672-0.357280356165-0.262462258344-0.4479212855380.8431421053680.03189036769340.2125790183891.008410305970.01700292475780.8611183631412.557657196894.180347280383.8702468162
348.63249645032.595619485447.751137072155.067125389824.983525081479.83216084887-0.0852399122501-0.600770977347-0.3811096911170.688001669773-0.4518368226121.09877490020.8676620238050.08515232347910.4901599788550.757076912962-0.05731181831680.1450569319341.267563409670.4914479107531.80367902117-20.268667791282.527631182893.0581376782
359.267856355935.715467083854.678497863633.901114891391.620546595546.56790737184-0.28378565664-0.318091717018-2.221549769080.1513811010440.445606172453-0.4565416283041.361302166790.530144386833-0.1377190396920.9309256289060.180795377230.4431699488641.228365559090.3170204892932.24108541739-8.3741916405977.187107284191.0896536779
367.85402824742.936020321464.376102424024.766036813372.256487417818.77907881236-0.736107281722-1.41523171801-0.920086687812-0.0989570961948-0.4289782209870.8087823112510.640604500153-0.3792219986620.9551421065720.757333802682-0.05067386905980.3050624244571.20572647980.2605634235821.59003735622-11.242060585186.333433880589.8080964631
374.448053426440.8025139850471.749124862181.22042901581.305107499079.227092186830.713255763196-0.480309099729-1.684286131370.551225635278-0.694395251236-0.1171706203751.99236798041-0.280246558849-0.0006193878398971.31426639188-0.007341640856080.2451670005291.13999019390.6017128540632.25942904925-16.471502472174.965951313296.3093945785
386.20769231995-0.921459425163-2.88965161828-0.0005065595430180.2441778798711.05996531435-0.1906436700530.577656847439-0.5133698600230.19054304160.1678671598170.4222735271440.142348432377-0.66847676432-0.02321923197120.687779490028-0.01836127665490.1256270727671.09133208352-0.0603400959651.02062319967-1.9300670888893.975480598671.4497734051
395.67684403222-1.28911908744-2.511360000035.302046089413.353269860186.71986116028-0.276767762412-0.312621188701-1.100970382350.531704663973-0.0173456566850.3375354052410.275125995813-0.6244251371180.6472245094390.6515537682590.06732140570130.2138941534211.121022322970.1945664523121.37521755393-22.283594343393.202498516786.9933113468
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 216 )
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 304 )
4X-RAY DIFFRACTION4chain 'A' and (resid 305 through 359 )
5X-RAY DIFFRACTION5chain 'A' and (resid 360 through 392 )
6X-RAY DIFFRACTION6chain 'A' and (resid 393 through 454 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 65 )
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 111 )
9X-RAY DIFFRACTION9chain 'B' and (resid 112 through 339 )
10X-RAY DIFFRACTION10chain 'B' and (resid 340 through 431 )
11X-RAY DIFFRACTION11chain 'B' and (resid 432 through 466 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 61 )
13X-RAY DIFFRACTION13chain 'C' and (resid 62 through 317 )
14X-RAY DIFFRACTION14chain 'C' and (resid 318 through 453 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 156 )
16X-RAY DIFFRACTION16chain 'D' and (resid 157 through 189 )
17X-RAY DIFFRACTION17chain 'D' and (resid 190 through 339 )
18X-RAY DIFFRACTION18chain 'D' and (resid 340 through 365 )
19X-RAY DIFFRACTION19chain 'D' and (resid 366 through 438 )
20X-RAY DIFFRACTION20chain 'D' and (resid 439 through 471 )
21X-RAY DIFFRACTION21chain 'E' and (resid 1 through 64 )
22X-RAY DIFFRACTION22chain 'E' and (resid 65 through 127 )
23X-RAY DIFFRACTION23chain 'E' and (resid 128 through 149 )
24X-RAY DIFFRACTION24chain 'E' and (resid 150 through 181 )
25X-RAY DIFFRACTION25chain 'E' and (resid 182 through 199 )
26X-RAY DIFFRACTION26chain 'E' and (resid 200 through 219 )
27X-RAY DIFFRACTION27chain 'F' and (resid 1 through 102 )
28X-RAY DIFFRACTION28chain 'F' and (resid 103 through 155 )
29X-RAY DIFFRACTION29chain 'F' and (resid 156 through 214 )
30X-RAY DIFFRACTION30chain 'H' and (resid 1 through 17 )
31X-RAY DIFFRACTION31chain 'H' and (resid 18 through 32 )
32X-RAY DIFFRACTION32chain 'H' and (resid 33 through 83 )
33X-RAY DIFFRACTION33chain 'H' and (resid 84 through 125 )
34X-RAY DIFFRACTION34chain 'H' and (resid 126 through 151 )
35X-RAY DIFFRACTION35chain 'H' and (resid 152 through 168 )
36X-RAY DIFFRACTION36chain 'H' and (resid 169 through 190 )
37X-RAY DIFFRACTION37chain 'H' and (resid 191 through 219 )
38X-RAY DIFFRACTION38chain 'L' and (resid 1 through 155 )
39X-RAY DIFFRACTION39chain 'L' and (resid 156 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