[English] 日本語
Yorodumi
- PDB-9cza: Crystal structure of integrin avb6 headpiece in complex with comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cza
TitleCrystal structure of integrin avb6 headpiece in complex with compound 18
Components
  • 17E6 Fab heavy chain
  • 17E6 Fab light chain
  • Integrin alpha-V heavy chain
  • Integrin beta-6
KeywordsCELL ADHESION/IMMUNE SYSTEM / avb6 integrin / fibrosis / idiopathic pulmonary fibrosis / free energy perturbation / CELL ADHESION / CELL ADHESION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


hard palate development / Langerhans cell differentiation / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / extracellular matrix protein binding / opsonin binding / enamel mineralization ...hard palate development / Langerhans cell differentiation / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / extracellular matrix protein binding / opsonin binding / enamel mineralization / integrin alphav-beta1 complex / bronchiole development / Cross-presentation of particulate exogenous antigens (phagosomes) / Laminin interactions / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / phospholipid homeostasis / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / regulation of phagocytosis / : / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / surfactant homeostasis / transforming growth factor beta binding / positive regulation of small GTPase mediated signal transduction / filopodium membrane / extracellular matrix binding / apolipoprotein A-I-mediated signaling pathway / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / Molecules associated with elastic fibres / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative chemotaxis / cell adhesion mediated by integrin / Syndecan interactions / microvillus membrane / skin development / lung alveolus development / cell-substrate adhesion / positive regulation of osteoblast proliferation / endodermal cell differentiation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / positive regulation of intracellular signal transduction / lamellipodium membrane / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / voltage-gated calcium channel activity / vasculogenesis / specific granule membrane / coreceptor activity / extrinsic apoptotic signaling pathway in absence of ligand / phagocytic vesicle / ERK1 and ERK2 cascade / positive regulation of cell adhesion / transforming growth factor beta receptor signaling pathway / substrate adhesion-dependent cell spreading / molecular function activator activity / 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 / integrin-mediated signaling pathway / cellular response to ionizing radiation / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cell morphogenesis / bone development / calcium ion transmembrane transport / cell-cell adhesion / response to virus / VEGFA-VEGFR2 Pathway / ruffle membrane / integrin binding / cell migration / virus receptor activity / positive regulation of cytosolic calcium ion concentration / protease binding / angiogenesis / receptor complex / cell adhesion / immune response / positive regulation of cell migration / inflammatory response / symbiont entry into host cell / external side of plasma membrane / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / extracellular exosome / metal ion binding
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2.
Similarity search - Domain/homology
: / ACETATE ION / alpha-D-mannopyranose / Integrin alpha-V / Integrin beta-6
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsMonroy, M.F. / Qiao, Q. / Lin, F.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: The Discovery of MORF-627, a Highly Selective Conformationally-Biased Zwitterionic Integrin alpha v beta 6 Inhibitor for Fibrosis.
Authors: Harrison, B.A. / Dowling, J.E. / Bursavich, M.G. / Troast, D.M. / Chong, K.M. / Hahn, K.N. / Zhong, C. / Mulvihill, K.M. / Nguyen, H. / Monroy, M.F. / Qiao, Q. / Sosa, B. / Mostafavi, S. / ...Authors: Harrison, B.A. / Dowling, J.E. / Bursavich, M.G. / Troast, D.M. / Chong, K.M. / Hahn, K.N. / Zhong, C. / Mulvihill, K.M. / Nguyen, H. / Monroy, M.F. / Qiao, Q. / Sosa, B. / Mostafavi, S. / Smukste, I. / Lee, D. / Cappellucci, L. / Konopka, E.H. / Nowakowski, P. / Stawski, L. / Senices, M. / Nguyen, M.H. / Kapoor, P.S. / Luus, L. / Sullivan, A. / Bortolato, A. / Svensson, M. / Hickey, E.R. / Konze, K.D. / Day, T. / Kim, B. / Negri, A. / Gerasyuto, A.I. / Moy, T.I. / Lu, M. / Ray, A.S. / Wang, L. / Cui, D. / Lin, F.Y. / Lippa, B. / Rogers, B.N.
History
DepositionAug 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-V heavy chain
B: Integrin beta-6
C: 17E6 Fab light chain
D: 17E6 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,78429
Polymers166,1034
Non-polymers5,68125
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.255, 132.058, 168.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Integrin alpha-V heavy chain


Mass: 66456.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA, VTNR / Production host: Homo sapiens (human) / References: UniProt: P06756
#2: Protein Integrin beta-6


Mass: 52714.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB6 / Production host: Homo sapiens (human) / References: UniProt: P18564

-
Antibody , 2 types, 2 molecules CD

#3: Antibody 17E6 Fab light chain


Mass: 23722.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Antibody 17E6 Fab heavy chain


Mass: 23209.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

-
Sugars , 6 types, 8 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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
#8: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
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
#10: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#14: 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: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 6 types, 94 molecules

#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#11: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#13: Chemical ChemComp-A1A6B / (2S)-(2-cyclopropylphenyl){(3R)-3-[4-(5,6,7,8-tetrahydro-1,8-naphthyridin-2-yl)butoxy]pyrrolidin-1-yl}acetic acid


Mass: 449.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N3O3
#15: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3O2
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 13% PEG 3350, 100 mM HEPES pH 7.1, 200 mM ammonium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.49→41.8 Å / Num. obs: 75921 / % possible obs: 99.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 54.62 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.16
Reflection shellResolution: 2.49→2.579 Å / Num. unique obs: 5546 / CC1/2: 0.361

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALS3.13.0data reduction
Aimless0.7.9data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→41.8 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2442 3724 4.92 %
Rwork0.2234 --
obs0.2244 75673 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11434 0 368 77 11879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312051
X-RAY DIFFRACTIONf_angle_d0.63716329
X-RAY DIFFRACTIONf_dihedral_angle_d17.5944450
X-RAY DIFFRACTIONf_chiral_restr0.0461859
X-RAY DIFFRACTIONf_plane_restr0.0032094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.520.35221410.33362592X-RAY DIFFRACTION98
2.52-2.550.36361390.32962613X-RAY DIFFRACTION100
2.55-2.590.33231440.3292636X-RAY DIFFRACTION100
2.59-2.630.34721420.31322596X-RAY DIFFRACTION99
2.63-2.670.33831300.31022645X-RAY DIFFRACTION100
2.67-2.710.33631460.32132597X-RAY DIFFRACTION100
2.71-2.750.31331250.31322663X-RAY DIFFRACTION100
2.75-2.80.35841330.31352613X-RAY DIFFRACTION100
2.8-2.850.33671490.30642642X-RAY DIFFRACTION100
2.85-2.90.32831390.29482647X-RAY DIFFRACTION100
2.9-2.960.32621340.27792640X-RAY DIFFRACTION100
2.96-3.030.28461340.28162640X-RAY DIFFRACTION100
3.03-3.10.25671370.25672647X-RAY DIFFRACTION100
3.1-3.180.27991320.26282644X-RAY DIFFRACTION100
3.18-3.260.29131370.27292673X-RAY DIFFRACTION100
3.26-3.360.2891470.2722631X-RAY DIFFRACTION100
3.36-3.470.2361250.2362690X-RAY DIFFRACTION100
3.47-3.590.27831450.2332653X-RAY DIFFRACTION100
3.59-3.730.23371330.21762684X-RAY DIFFRACTION100
3.73-3.90.23911290.2082681X-RAY DIFFRACTION100
3.9-4.110.21351290.19582678X-RAY DIFFRACTION100
4.11-4.370.19851470.17842682X-RAY DIFFRACTION100
4.37-4.70.19521530.16142680X-RAY DIFFRACTION100
4.7-5.180.17891390.15932699X-RAY DIFFRACTION100
5.18-5.920.1971420.17872737X-RAY DIFFRACTION100
5.92-7.450.22331240.20842781X-RAY DIFFRACTION100
7.46-41.80.21391490.19242865X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.47870.20390.47571.14680.12771.5077-0-0.2042-0.11840.0763-0.04480.11330.0979-0.2730.04130.32720.00460.03280.43250.01780.38617.6857-38.1208-1.3759
29.0327.4372-2.62198.4056-2.05952.3960.3365-0.1843-1.1120.2607-0.2948-1.21230.25740.2271-0.02710.51060.0854-0.02980.5633-0.0550.608532.0325-34.704318.3246
34.3242.67590.05047.6384-0.76861.907-0.0368-0.09090.79250.2706-0.1660.4802-0.3566-0.16890.20770.56610.0974-0.01030.66-0.0770.460227.7397-14.204717.5589
43.8779-0.2511-0.39518.331-5.10814.0302-0.02130.1006-0.19330.72730.1119-1.02010.1378-0.1661-0.08071.0094-0.0055-0.15780.6444-0.11580.970142.209719.323719.4073
54.98641.217-3.03354.0872-2.1023.17780.28360.6562-0.2008-0.8281-0.2720.86570.5486-1.4583-0.03580.8270.1069-0.22180.7865-0.13110.642-5.1599-47.1066-67.5725
62.7291-1.4126-0.39593.18551.26476.51850.11050.45120.0341-0.4644-0.39960.3035-0.1082-0.67520.28080.54490.1081-0.15290.5129-0.06280.4862-0.5211-41.505-61.5569
70.8871-0.9872-1.03641.9352.56428.14490.29880.333-0.1727-0.4361-0.41170.2148-0.2031-0.89660.08710.4960.075-0.11970.538-0.05330.4169-0.5625-49.953-67.6623
84.2416-4.53260.31798.3286-0.51732.00280.25480.6346-0.391-0.1921-0.57020.9462-0.0901-0.45770.30430.53760.0952-0.06750.7282-0.14910.60169.9916-69.7019-85.711
93.6748-1.9233-0.92246.20220.2593.3741-0.16430.5393-0.22050.0272-0.01930.76210.0003-0.26160.20150.56050.1115-0.07920.7567-0.09830.61655.7698-65.1894-81.6064
105.6256-5.10881.83286.9935-2.01854.55360.37370.434-0.8125-0.9187-0.44951.49070.0822-0.49420.04410.47690.0382-0.12610.8383-0.26470.83966.8127-75.6689-89.9068
113.65784.0559-0.74749.5527-1.45053.08590.1707-0.2356-0.4502-0.1099-0.5828-1.44230.60750.47890.40380.73220.2042-0.09830.6819-0.01330.433118.6966-57.6395-54.2653
121.835-1.4921-0.41575.26342.70592.93980.0886-0.0805-0.26210.2653-0.13270.15650.7330.03740.03610.56740.0227-0.09440.37240.0230.354811.384-55.5449-49.6129
135.4443-1.2546-1.16865.9133-0.84925.436-0.17910.3620.18590.0663-0.122-0.7367-0.09170.01370.2620.4510.0462-0.0560.4403-0.07290.537322.2482-66.1432-82.0849
142.22841.36070.34623.02760.61432.2422-0.15920.18260.2963-0.19250.02830.1946-0.3357-0.13690.1370.38630.0604-0.09570.39260.05320.37497.924-17.7034-34.2856
150.83160.33760.1970.80.41430.4229-0.06440.04420.1477-0.0077-0.006-0.0961-0.18620.07450.07230.4409-0.0144-0.07820.43790.08220.450327.2418-18.481-23.6346
163.30891.23381.81953.80250.96494.0668-0.4041-0.10310.845-0.41650.28360.1836-0.5501-0.25430.18740.65750.0541-0.11570.5334-0.02870.88747.844417.8581-10.1091
177.15881.57210.47326.40730.3915.3837-0.2137-0.1093-0.93210.7455-0.2673-1.8612-0.48240.72280.50890.85270.0221-0.23460.59840.13971.181648.38230.877220.1249
183.7241.46460.67084.1966-0.33582.55080.2456-0.60710.26670.9657-0.27650.0224-0.3743-0.42110.04990.61260.05680.01920.6591-0.06890.340426.1005-21.199326.3792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 116 through 368 )
2X-RAY DIFFRACTION2chain 'B' and (resid 369 through 396 )
3X-RAY DIFFRACTION3chain 'B' and (resid 397 through 441 )
4X-RAY DIFFRACTION4chain 'B' and (resid 442 through 477 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 18 )
6X-RAY DIFFRACTION6chain 'C' and (resid 19 through 90 )
7X-RAY DIFFRACTION7chain 'C' and (resid 91 through 113 )
8X-RAY DIFFRACTION8chain 'C' and (resid 114 through 149 )
9X-RAY DIFFRACTION9chain 'C' and (resid 150 through 174 )
10X-RAY DIFFRACTION10chain 'C' and (resid 175 through 214 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 16 )
12X-RAY DIFFRACTION12chain 'D' and (resid 17 through 124 )
13X-RAY DIFFRACTION13chain 'D' and (resid 125 through 217 )
14X-RAY DIFFRACTION14chain 'A' and (resid 1 through 149 )
15X-RAY DIFFRACTION15chain 'A' and (resid 150 through 460 )
16X-RAY DIFFRACTION16chain 'A' and (resid 461 through 595 )
17X-RAY DIFFRACTION17chain 'B' and (resid 5 through 51 )
18X-RAY DIFFRACTION18chain 'B' and (resid 52 through 115 )

+
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