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- PDB-7ukp: Integrin alpha IIB beta3 complex with a gantofiban analog -

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Basic information

Entry
Database: PDB / ID: 7ukp
TitleIntegrin alpha IIB beta3 complex with a gantofiban analog
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 / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / 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 / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / blood coagulation, fibrin clot formation / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / glycinergic synapse / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / positive regulation of bone resorption / filopodium membrane / extracellular matrix binding / negative regulation of low-density lipoprotein particle clearance / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / regulation of bone resorption / positive regulation of leukocyte migration / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of fibroblast migration / integrin complex / positive regulation of smooth muscle cell migration / heterotypic cell-cell adhesion / smooth muscle cell migration / Molecules associated with elastic fibres / negative chemotaxis / positive regulation of cell-matrix adhesion / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / Syndecan interactions / cell adhesion mediated by integrin / p130Cas linkage to MAPK signaling for integrins / positive regulation of osteoblast proliferation / cellular response to insulin-like growth factor stimulus / protein disulfide isomerase activity / regulation of postsynaptic neurotransmitter receptor internalization / microvillus membrane / cell-substrate adhesion / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / TGF-beta receptor signaling activates SMADs / fibronectin binding / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / positive regulation of T cell migration / 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 / Integrin signaling / embryo implantation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of smooth muscle cell proliferation / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / wound healing / cellular response to mechanical stimulus / Signaling by high-kinase activity BRAF mutants / cell-cell adhesion / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet activation / platelet aggregation / VEGFA-VEGFR2 Pathway / ruffle membrane / cellular response to xenobiotic stimulus / integrin binding / positive regulation of fibroblast proliferation
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrin alpha cytoplasmic region / Integrins beta chain EGF (I-EGF) domain profile. / 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) / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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 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-NJ9 / Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.80112979054 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)302,35636
Polymers297,4068
Non-polymers4,95028
Water5,891327
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)151,19317
Polymers148,7034
Non-polymers2,49013
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)151,16319
Polymers148,7034
Non-polymers2,46015
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)259.322, 144.495, 104.848
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

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Components

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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

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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)

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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

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Non-polymers , 6 types, 349 molecules

#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / 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.: 4 / Source method: obtained synthetically / Formula: Mn
#12: Chemical ChemComp-NJ9 / 3-(4-{[(5S)-3-(4-carbamimidoylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}piperazin-1-yl)propanoic acid


Mass: 375.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H25N5O4 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.76 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 96001 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 86.0179738794 Å2 / CC1/2: 0.989 / Net I/σ(I): 5.48
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 14555 / CC1/2: 0.112

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Processing

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

3t3p


Resolution: 2.80112979054→48.2519232278 Å / SU ML: 0.472994803202 / Cross valid method: FREE R-VALUE / σ(F): 1.32632618099 / Phase error: 29.7782149905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24076472953 1983 2.11490673293 %
Rwork0.218951192265 91780 -
obs0.219411892317 93763 96.1257714625 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.471628379 Å2
Refinement stepCycle: LAST / Resolution: 2.80112979054→48.2519232278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20715 0 297 327 21339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059012490695621650
X-RAY DIFFRACTIONf_angle_d0.57502623937429407
X-RAY DIFFRACTIONf_chiral_restr0.04360625072623274
X-RAY DIFFRACTIONf_plane_restr0.004096617213663807
X-RAY DIFFRACTIONf_dihedral_angle_d11.679286185612880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.80112979054-2.87120.4387669713941170.4003905295075509X-RAY DIFFRACTION81.9280617446
2.8712-2.94880.3888363220341330.38480439776172X-RAY DIFFRACTION91.5625907639
2.9488-3.03550.4057723700791380.3535104062056306X-RAY DIFFRACTION93.5675911137
3.0355-3.13350.3725056815731390.3326121237446450X-RAY DIFFRACTION95.2856109906
3.1335-3.24550.3250371239911410.3127603846576515X-RAY DIFFRACTION96.338109712
3.2455-3.37540.3114857683551420.2846101548476541X-RAY DIFFRACTION96.7849384504
3.3754-3.5290.2596120228111420.2495362496456591X-RAY DIFFRACTION97.4103009259
3.529-3.7150.2258858238231430.2334191715426624X-RAY DIFFRACTION97.7184115523
3.715-3.94760.2102440990111450.2241856187416694X-RAY DIFFRACTION98.8294797688
3.9476-4.25220.2358549208831460.2050982656866755X-RAY DIFFRACTION98.7550085861
4.2522-4.67980.2009581617791470.1854817370886802X-RAY DIFFRACTION99.6844068283
4.6798-5.35630.2033277819311480.1845184619536822X-RAY DIFFRACTION99.4435725496
5.3563-6.74540.2496863597471480.207836179736899X-RAY DIFFRACTION99.449618967
6.7454-48.25192322780.2043273867971540.1737889863297100X-RAY DIFFRACTION98.5463931531
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)
12.995539430260.19743057416-0.09400056933131.88081024537-0.05275197582312.070193095960.1370897192120.2625359950610.0781414431111-0.321619810067-0.1032846127420.5537849855910.0698570158217-0.241427372275-1.86026197267E-50.7194841742970.06233930227850.05059763033770.6010016184410.03958965532930.85969592223646.654970219290.309010516538.4965013321
22.42808330165-0.700482406375-0.3932470518781.647429928440.2297722444081.443963808090.130742571182-0.1779450834460.01662996029290.435914638676-0.2017105701740.3601169169530.220206239825-0.1827007324451.35316091178E-50.816515350703-0.07983487910420.1833073716110.5208047474380.0009637388711040.78551166125645.287510400892.895035664862.4782621872
32.007329839620.1616983912930.05593540685622.719201245470.464405984563.030021961830.02059370854840.0906086760516-0.241784079515-0.0418264420693-0.0340896876788-0.0609691719430.3236929728420.121118647543.34163996374E-50.7476413719630.08004812322060.06965755151680.4577799901450.0524005925920.69938834891364.466721382183.397595439947.1465143594
41.846309515710.983652944338-0.1078822636780.5862230845950.4509998191531.97915984317-0.0982414365142-0.04170231774490.2455014933840.1175485034850.549121256157-0.7479089764080.01202777049211.634152804950.0002654484698940.9475471567320.148418686691-0.05468553886731.82689420365-0.04925768423361.29901251941113.760064855100.59254129343.42154166
52.195019637010.8629039229180.284761454543.496341709570.6393634131931.627559053540.0793858699419-0.1494643014960.3440823271680.276885024476-0.0524881036476-0.0271292403297-0.267459595540.0375056871587-0.0001717583269460.7669312517360.02593001452490.09700688248840.4490416283640.01121752031920.78655822779867.0516721664117.53825240863.3631844769
61.44195695266-0.29727217279-0.8344894339990.697989700806-0.3440516899110.810698646963-0.0887826541899-0.22719555546-0.08417950334780.09026368140720.00552311206554-0.2450843275060.313566629121.08235768917-2.07213258611E-50.9769491476760.12001121652-0.129796960041.24121654687-0.04080896874311.2157745044597.0547444639105.87829246656.6118999853
70.283988082995-0.00911766974640.2347756123390.0649616344684-0.00143383939670.1599648899580.116636494544-0.3044693801790.27809744698-0.4013450714930.333118858446-0.8600430350770.5840584681650.211590547050.0003065164697241.414432729780.3275941815360.2097407900342.396042999120.06933560112441.44585972127115.90504928889.145779680419.4488555816
82.63849993956-0.0539549521667-1.088223557351.905827285190.857771209731.35795889054-0.139728389212-0.090499892791-0.0210337153202-0.026370175248-0.0852814468256-0.3712433448020.1552043341640.82043573043-1.20342794947E-50.7621248257820.08374563823210.05671507690440.8854454862480.06546201345470.88262738324187.890207789494.7486606884131.961307337
93.16865718730.542215680768-0.3615394665061.03005640773-0.8578367812042.54971749176-0.3414361441520.718277785866-0.195367899159-0.471045966813-0.0624308969456-0.2649199292540.4769131483430.3637634291647.00085746385E-60.9896180062150.07598836560750.2281874093321.08121791412-0.01237622232420.83303967937390.569712796389.1547219322107.754705315
103.38659172044-0.2331640859070.3466800585832.345641387870.3608408180753.25065755852-0.3043011784770.086482722933-0.605548006752-0.11264150090.0507106957679-0.02066642943140.788716202951-0.0125627770261-0.0006101893350190.9970557725080.02501135240120.2225921776520.660024644803-0.01800250610270.82940725640773.945363582379.2665893767126.96209344
111.74588361507-0.852793611091-0.6441371086640.3543506391460.2544018679981.24123643798-0.5514889763850.644243164757-0.00796534586233-0.2728506464890.1626013671850.4520999246910.730781954142-1.34792010861-0.0001396146429161.32575659391-0.530160610813-0.07211951831191.84980614517-0.05601583959231.3265681687620.311313848180.2553651425129.76647929
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140.2278666588140.29138889859-0.01374052094460.3669269859440.03485448661170.0642045921266-0.52041353377-0.708735035295-0.8362638447790.5681622592170.0492198272950.692210010880.546208120338-1.035989817570.0002802962109661.67346318034-0.276027174860.2105650923571.41691237537-0.1870093373481.7684458059821.942382428777.9022831509157.360434162
150.3013539692050.07571720734320.03004355241020.01955971786140.04832504699970.07695517961290.2701526692181.02908430934-0.884787133119-0.54331100327-0.1952183406650.3063076979540.3185928112760.022966697455-0.0004903209386821.292433489290.1490875739630.2088278450671.564173888530.05200714078471.35683634262120.07312250582.754424902383.1088461762
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170.0928434011002-0.03233398950370.08518432869340.1935822818570.08899812992820.1496161029190.1953089853920.2988560203490.112277435486-0.678453147944-0.33973999846-0.5766094133760.2522522677310.227434772239-8.41837122526E-51.15602891202-0.005591637699750.3075317728381.764003235850.1936131470831.19326009811117.1156672195.626485279687.0362893908
180.0255179233956-0.0319408419462-0.03601732090080.03595952690550.03409450972180.01679221609440.05738397818990.689929099799-0.270351862852-0.263142794741-0.7142444309620.3637706643530.429712470843-0.205624373542-0.0003179187737161.191936581120.0853431220630.1422898306721.821656014940.09846298747061.10878146188107.800374996.773938094782.5261257013
190.46243065575-0.1880232817840.4505806843680.260271442097-0.2268162129270.403969027310.08295061304780.9175826608920.250835682381-0.102742046749-0.05273345060670.2175078697340.5327141012450.1212219658970.0001195494589851.38271455704-0.001246711787450.3230657458851.882800226040.08276044658811.12277888017114.13594108989.467262933187.4761949496
200.01081796948390.03312185375810.004823020580520.07478736884460.01442219730260.08044145383070.3127924705210.662420648994-0.587122019480.1852371415080.360670150935-0.3589678782610.720310381341.007563666850.0006180435100291.668987457990.2282614425910.1770863689542.30160473619-0.1170287017121.23544682696131.09144472584.460731122772.0602712953
210.0187905400722-0.102017747268-0.0276797255340.2377917275290.1887098772320.211879748154-0.7677198910941.25432645638-0.2310115856020.1249405778340.741368270332-0.6345155757010.3402232734210.6229906454570.0004728642305952.151111623560.6443999113510.06452873887332.398034446280.0005372105664741.62320502787150.95007596582.204654178179.306852652
220.0314298904242-0.0232309099332-0.03251785704670.01404013523860.003561104572780.04335700487870.1055990411280.066921263826-0.115964729794-0.201123086222-0.509439166624-0.44397634212-0.234512982194-0.194415514076-0.0001301625941351.581701915990.3649813825080.1895426123892.61397020210.2424697090041.47506205411147.22010991385.757553375586.766977771
230.1269270931910.178658598008-0.03527209633010.26527076791-0.02721639675610.05132455213090.6106623068370.259357637592-0.174151141092-0.256845604780.165035133845-0.1103666866230.1319520921260.540485831852-8.4400454046E-51.796324758630.9180974435610.1282725715172.51981664030.1729621194381.69776714055153.36313453183.609070923881.1584827953
240.02095724778870.051214890947-0.02603906209330.0487680198385-0.06378606325270.03297698888670.321404453717-0.1193879127750.1822885817450.01004199134220.178943356759-1.10322613757-0.1827728146670.65585216114-0.000417484927951.715859520171.18701170179-0.2721452341473.26885965796-0.4708405133841.64890064793150.54330533976.20078415275.5460251352
250.09900821666160.0146724570851-0.1266710264330.1319190596290.04760952839930.1586183997960.29138180741-0.503568541080.399570234188-0.2722684749580.606598512358-0.284770709008-0.3819864407490.914905363070.0001354410200221.11021227127-0.03128634843550.2139483311062.00297293793-0.00776563478721.69291388607131.39672773103.650998556100.510891081
260.2238404594210.05092340715880.1249319978040.03891405466530.007756586090240.0801441481264-0.1287605587540.1089801468361.43008008945-0.152741705490.302284061921-0.6560947022350.4975402513220.5983722838160.0005014915293180.914904343139-0.04047314428070.1458974635151.750531892920.1178778151991.52419458696121.571139552104.236015589100.86646257
270.376307081949-0.2717011630980.2178751781370.256415891392-0.01245852235840.308364496803-0.0833796348146-0.2822877024550.3670699072170.8238651746630.117328555362-0.200230251531-0.006341041133140.422671832629-3.91038794963E-51.03550979002-0.06786092545930.06698385998151.641685579730.07590887303941.21959454119122.41799444396.5532994349105.513553668
280.09232607307710.06628777603390.1608772180730.03192382274210.1279616414380.220086399194-0.09951492499420.01578299010160.7009631094260.006009130003080.101009612259-0.6323557993090.07396178648971.00162915591-0.0001311257675371.006550658370.006679020847970.2260995634711.879593795220.06878263002241.20987335344124.60821811198.384292628698.8065239786
290.31632245251-0.08156062234990.3309661923430.3111935704750.01042005510480.364173188229-0.1937075849730.5801639416340.167585053508-0.503399952203-0.2984906222770.22299273258-0.2009171469961.08756418688-0.05880084568420.8034643818820.2335996751750.2057590225133.008197377690.2390930054491.715345523146.70082694598.069157836599.5533625428
300.05195817708410.222129009450.04278568089220.9186589082430.1998073518490.0397095978918-0.247355044629-0.4159619634630.189250532113-0.408512670819-0.04727344601540.216551110226-0.2110782557830.1662423842760.0184982932041.738227807561.002875338350.592320485963.78623556230.1149458783231.65265837729156.68783438388.885743726472.2033750917
310.09051718229650.0373128956966-0.0137277921840.0351221928908-0.02180706896350.0116126761714-0.06509770121610.927516934006-0.120455844475-0.365668178156-0.065613567351-0.271362345431-0.04334969510030.6883800972276.20933465548E-51.667387691730.120348166950.2518336851112.957218025880.3686977923511.22909368749151.14545067796.414593008786.8699168699
320.00536934609766-0.00896872470590.002423556097990.006802300100580.00319868407170.0127976178864-0.14808107344-0.3278242000710.315002170978-0.2056469014730.443654604151-0.423065496998-0.0960519048531-0.189706513386-0.0002125382163872.213088347240.1131227417340.837233754162.232171927180.6098538519012.07133076216154.46235983105.66703909175.2625630302
33-0.0155596270170.02900905010060.003884048414190.09056067000020.009437430382490.03253644647280.4775724985050.653956560094-0.00328109102443-1.09556858647-0.005270901188370.245628955055-0.654634886655-0.2337552557960.0005500613485561.351942110710.1094156257720.1727024600472.324419007870.4375381265921.78970269393146.13994353794.440254768887.9135131565
34-0.0218068112792-0.025898498499-0.00315811978976-0.003979450868550.0129577792366-0.0178897873271-0.1210768721551.277336450270.561978621276-0.613079288613-0.353591518945-0.739494901847-0.4085581641911.08847746799-0.01228177625571.50462829058-0.06562777859130.5724831038963.223488989420.2964195536051.86835844654158.14407356799.387777441575.0673220933
350.327699837402-0.0697081950450.06860638236920.204588488856-0.2138742471550.20289557794-0.616673408919-0.6890042454660.1272446071790.398214510920.281340098393-0.0773913600646-0.03005872924980.3723571660980.0003376086612681.4044419418-0.04539836028720.2559289305481.26671466626-0.04221766323161.1916230754815.113723494589.719148964189.4177627212
360.329632888340.6401742578440.1135265177841.24345575249-0.09152557183621.2789488177-0.0596863973166-0.3264594530440.02381928595820.3140071468610.0583870884363-0.02169396140060.332954495785-0.08790539860184.69700433616E-50.8301732592060.01590589037530.1823117152571.10217859227-0.1753681948281.0438057754220.657371682696.880159046681.1676779743
370.3228202670260.242540338753-0.1966632573760.196510934602-0.1254369038330.1144237077770.301705486289-0.690803700285-0.1357604838220.27197867463-0.0891135561046-0.00389168689024-0.2274890003790.328487986991-9.6880419856E-51.149169835860.1189024196350.1212779625661.17499531747-0.0530293353951.093206146222.308881601998.822297853287.3919467712
380.923881115228-0.3829677361490.09741354110750.353198334888-0.2950402986990.1929097751240.0345046809608-0.544837198593-0.1243317972770.3459186710860.1226882297940.1608122119620.1309939457240.188067893069-3.21961260528E-50.996377178551-0.02830684714030.231824310871.11606498335-0.03047807830481.125399253512.779759224794.31059790784.3621456209
390.263189321246-0.367291995965-0.1561630705480.6703599211950.5236753298130.465440104895-0.0342307786737-0.667776445365-1.761885255630.4268361703120.2954791761990.3607826563540.9032273855440.162316543820.0003505322057571.083163104980.03566587202610.09655746375151.187697307130.3756058158882.167901789-15.136971107480.389913055792.343871359
400.112420511339-0.1076165448840.06831121420850.242813596041-0.2364463899250.227733373672-0.63534968422-1.07957727616-0.7836425232440.01584954062570.2169718463170.7333792874890.429686381910.0384805397472-0.000210193080390.916872479790.1567178847920.03032057639571.186950812080.1582773830831.57661790752-8.7799014901589.593588477490.1489887862
410.07633406702260.0411099149608-0.08164458639050.000135677810392-0.008638741472410.277831924791-0.132893251303-0.163377735578-2.312164317140.3280317150880.0583889630314-0.4392270610341.089823018190.1770803570330.00149034483151.22510260783-0.103254785140.1701390835031.231920103030.5178914314032.24204367845-15.842712867577.343273187894.6442893636
420.136844337641-0.109500336053-0.06145597246830.168683577265-0.04721065638660.09156855317410.06742327653420.5845875027230.263736498209-0.468590874385-0.07474080407120.668352131554-0.445853679665-0.881552083392-0.0006783446979250.9191219129630.07557343718720.0653141647631.46640145763-0.2913400134661.516164872410.22395208978497.623735458664.8931872784
430.8583464368720.07408937260280.2463725194030.2354435925530.2879712076960.327735642858-0.1287751819510.5108449357630.010232314775-0.1267839022950.1846915028220.2136822519380.101689916296-0.719740817002-3.89933320765E-50.798882642092-0.08180222228780.09251239988741.1985770726-0.1545146531641.1932698058910.510406310195.193753774363.4135563271
440.1389863291040.0113524279454-0.01607827612550.0560863447510.03231160671420.0899079963245-0.00343514969435-0.111129360988-0.64937484408-0.013535881492-0.1775339482160.723547459770.234121937908-0.8722634689670.0004211229868750.803669962015-0.1397646051430.1756332465921.52848475698-0.20157700581.33737289893.8774644550289.667396792166.1238303555
450.2327749946420.100631509278-0.2252662119880.0112384884424-0.03127468629090.1495119101870.07128151238260.5228819793840.487172288454-0.249988188642-0.2601299627460.672537013933-0.114199057425-0.6015333797627.51608943378E-50.807888818712-0.1324734325990.09411048905771.32416697643-0.2206882975021.33744068440.71097207392696.179059046269.7856489876
461.024923192190.09376342652180.275308611570.517872058850.1503038997280.502456023586-0.349198399603-0.105773065144-1.449002035760.3490580761860.08960052275520.454231359319-0.0676188893573-0.191770390638-0.0002067904729110.9081119361980.03822933874520.3386887004341.218284786060.2417820073451.66606026814-21.765895887192.556465332788.3685321961
471.48491431844-0.477257924450.8994429567861.54747752909-0.1254949333921.006527934270.00326898692972-0.534206372828-1.257359157150.335069171124-0.2045747385660.240448874552-0.0744896569847-0.474222273104-7.22506935672E-50.833181555068-0.05736799049380.2071587408051.345499363390.1103871655381.5937708912-22.400052605593.481563568687.0389721971
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 313 )
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 454 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 111 )
5X-RAY DIFFRACTION5chain 'B' and (resid 112 through 339 )
6X-RAY DIFFRACTION6chain 'B' and (resid 340 through 431 )
7X-RAY DIFFRACTION7chain 'B' and (resid 432 through 466 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 67 )
9X-RAY DIFFRACTION9chain 'C' and (resid 68 through 291 )
10X-RAY DIFFRACTION10chain 'C' and (resid 292 through 453 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 105 )
12X-RAY DIFFRACTION12chain 'D' and (resid 106 through 339 )
13X-RAY DIFFRACTION13chain 'D' and (resid 340 through 438 )
14X-RAY DIFFRACTION14chain 'D' and (resid 439 through 471 )
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 16 )
16X-RAY DIFFRACTION16chain 'E' and (resid 17 through 32 )
17X-RAY DIFFRACTION17chain 'E' and (resid 33 through 52 )
18X-RAY DIFFRACTION18chain 'E' and (resid 53 through 67 )
19X-RAY DIFFRACTION19chain 'E' and (resid 68 through 112 )
20X-RAY DIFFRACTION20chain 'E' and (resid 113 through 125 )
21X-RAY DIFFRACTION21chain 'E' and (resid 126 through 165 )
22X-RAY DIFFRACTION22chain 'E' and (resid 166 through 175 )
23X-RAY DIFFRACTION23chain 'E' and (resid 176 through 199 )
24X-RAY DIFFRACTION24chain 'E' and (resid 200 through 219 )
25X-RAY DIFFRACTION25chain 'F' and (resid 1 through 18 )
26X-RAY DIFFRACTION26chain 'F' and (resid 19 through 38 )
27X-RAY DIFFRACTION27chain 'F' and (resid 39 through 75 )
28X-RAY DIFFRACTION28chain 'F' and (resid 76 through 102 )
29X-RAY DIFFRACTION29chain 'F' and (resid 103 through 113 )
30X-RAY DIFFRACTION30chain 'F' and (resid 114 through 129 )
31X-RAY DIFFRACTION31chain 'F' and (resid 130 through 144 )
32X-RAY DIFFRACTION32chain 'F' and (resid 145 through 155 )
33X-RAY DIFFRACTION33chain 'F' and (resid 156 through 174 )
34X-RAY DIFFRACTION34chain 'F' and (resid 175 through 214 )
35X-RAY DIFFRACTION35chain 'H' and (resid 1 through 17 )
36X-RAY DIFFRACTION36chain 'H' and (resid 18 through 60 )
37X-RAY DIFFRACTION37chain 'H' and (resid 61 through 83 )
38X-RAY DIFFRACTION38chain 'H' and (resid 84 through 125 )
39X-RAY DIFFRACTION39chain 'H' and (resid 126 through 168 )
40X-RAY DIFFRACTION40chain 'H' and (resid 169 through 179 )
41X-RAY DIFFRACTION41chain 'H' and (resid 180 through 219 )
42X-RAY DIFFRACTION42chain 'L' and (resid 1 through 18 )
43X-RAY DIFFRACTION43chain 'L' and (resid 19 through 75 )
44X-RAY DIFFRACTION44chain 'L' and (resid 76 through 90 )
45X-RAY DIFFRACTION45chain 'L' and (resid 91 through 113 )
46X-RAY DIFFRACTION46chain 'L' and (resid 114 through 155 )
47X-RAY DIFFRACTION47chain 'L' and (resid 156 through 214 )

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  • 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

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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

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