[English] 日本語
Yorodumi
- PDB-4mmx: Integrin AlphaVBeta3 ectodomain bound to the tenth domain of Fibr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mmx
TitleIntegrin AlphaVBeta3 ectodomain bound to the tenth domain of Fibronectin
Components
  • Fibronectin
  • Integrin alpha-VIntegrin alpha V
  • Integrin beta-3Integrin beta 3
KeywordsCELL ADHESION / integrin / A domain / hybrid domain / PSI / EGF repeats / beta TA thigh / beta propeller / RGD motif / fibronectin / vitronectin
Function / homology
Function and homology information


integrin alphav-beta6 complex / integrin alphav-beta8 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex ...integrin alphav-beta6 complex / integrin alphav-beta8 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / 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 / neural crest cell migration involved in autonomic nervous system development / regulation of postsynaptic neurotransmitter receptor diffusion trapping / peptidase activator activity / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / Laminin interactions / positive regulation of glomerular mesangial cell proliferation / regulation of extracellular matrix organization / platelet alpha granule membrane / fibrinogen complex / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / peptide cross-linking / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / glycinergic synapse / integrin activation / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / blood coagulation, fibrin clot formation / negative regulation of lipid transport / ALK mutants bind TKIs / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / regulation of phagocytosis / cell-substrate junction assembly / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / angiogenesis involved in wound healing / platelet-derived growth factor receptor binding / filopodium membrane / positive regulation of small GTPase mediated signal transduction / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of postsynaptic neurotransmitter receptor internalization / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / wound healing, spreading of epidermal cells / apoptotic cell clearance / heterotypic cell-cell adhesion / integrin complex / positive regulation of cell adhesion mediated by integrin / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / cellular response to insulin-like growth factor stimulus / positive regulation of intracellular signal transduction / proteoglycan binding / positive regulation of cell-matrix adhesion / cell adhesion mediated by integrin / smooth muscle cell migration / microvillus membrane / extracellular matrix structural constituent / MET activates PTK2 signaling / Syndecan interactions / negative chemotaxis / p130Cas linkage to MAPK signaling for integrins / cellular response to platelet-derived growth factor stimulus / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of smooth muscle cell migration / endodermal cell differentiation / 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 / Non-integrin membrane-ECM interactions / fibronectin binding / Signaling by ALK fusions and activated point mutants / basement membrane / positive regulation of cell adhesion
Similarity search - Function
Hormone receptor fold - #30 / ntegrin, alpha v. Chain A, domain 4 / Integrin domains. Chain A, domain 2 / Hormone receptor fold / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. ...Hormone receptor fold - #30 / ntegrin, alpha v. Chain A, domain 4 / Integrin domains. Chain A, domain 2 / Hormone receptor fold / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / 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) / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Integrin alpha cytoplasmic region / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha 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 / Laminin / Laminin / 7 Propeller / Methylamine Dehydrogenase; Chain H / Kringle-like fold / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Few Secondary Structures / Irregular / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Fibronectin / Integrin beta-3 / Integrin alpha-V
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
Authorsvan Agthoven, J. / Xiong, J. / Arnaout, M.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural basis for pure antagonism of integrin alpha V beta 3 by a high-affinity form of fibronectin.
Authors: Van Agthoven, J.F. / Xiong, J.P. / Alonso, J.L. / Rui, X. / Adair, B.D. / Goodman, S.L. / Arnaout, M.A.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Apr 30, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-V
B: Integrin beta-3
C: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,90825
Polymers192,9213
Non-polymers6,98722
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16100 Å2
ΔGint49 kcal/mol
Surface area79550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.859, 129.859, 305.831
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein Integrin alpha-V / Integrin alpha V / Vitronectin receptor subunit alpha / Integrin alpha-V heavy chain / Integrin alpha-V light chain


Mass: 106048.359 Da / Num. of mol.: 1 / Fragment: Extracellular domain (UNP residues 31-989)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: alphav, ITGAV, MSK8, VNRA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P06756
#2: Protein Integrin beta-3 / Integrin beta 3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 76523.125 Da / Num. of mol.: 1 / Fragment: Extracellular domain (UNP residues 27-718)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GP3A, ITGB3 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P05106
#3: Protein Fibronectin / / FN / Cold-insoluble globulin / CIG


Mass: 10349.573 Da / Num. of mol.: 1
Fragment: Fibronectin type-III domain 10 (UNP residues 1448-1540)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Fibronectin, FN, FN1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P02751

-
Sugars , 5 types, 14 molecules

#4: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-6)-[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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DManpb1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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]/1-1-2-3-2-3/a4-b1_b4-c1_c3-d1_c6-e1_e4-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{[(4+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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 , 2 types, 10 molecules

#9: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 12% PEG3350, 0.8 M sodium chloride, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2012
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 3.32→75.49 Å / Num. all: 67157 / Num. obs: 39593 / % possible obs: 88 % / Observed criterion σ(F): 5.3 / Observed criterion σ(I): 5.3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 13.9
Reflection shellResolution: 3.32→3.41 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.676 / % possible all: 88

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→42.506 Å / SU ML: 0.42 / σ(F): 1.38 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 1942 4.91 %
Rwork0.2082 --
obs0.2105 39586 88 %
all-39661 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.32→42.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13184 0 440 2 13626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114004
X-RAY DIFFRACTIONf_angle_d0.86418917
X-RAY DIFFRACTIONf_dihedral_angle_d12.4765175
X-RAY DIFFRACTIONf_chiral_restr0.0352172
X-RAY DIFFRACTIONf_plane_restr0.0042445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.4030.34421470.2823003X-RAY DIFFRACTION100
3.403-3.4950.3324850.29251356X-RAY DIFFRACTION46
3.495-3.59780.33791660.25922984X-RAY DIFFRACTION100
3.5978-3.71380.3559470.25321222X-RAY DIFFRACTION40
3.7138-3.84650.28791270.24943018X-RAY DIFFRACTION100
3.8465-4.00040.3271820.23111431X-RAY DIFFRACTION47
4.0004-4.18230.23181520.21323046X-RAY DIFFRACTION100
4.1823-4.40260.22551380.19153033X-RAY DIFFRACTION100
4.4026-4.67810.21871730.16743029X-RAY DIFFRACTION100
4.6781-5.03880.22141750.16773027X-RAY DIFFRACTION100
5.0388-5.54490.24321840.18913037X-RAY DIFFRACTION100
5.5449-6.34490.27681590.21883077X-RAY DIFFRACTION100
6.3449-7.98530.28661680.22723125X-RAY DIFFRACTION100
7.9853-42.50990.23171390.19413256X-RAY DIFFRACTION99
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)
14.39060.88840.69573.0593-0.59392.1627-0.35520.26450.2765-0.22350.2243-0.0609-0.46530.1520.14250.6904-0.2076-0.02710.35330.0160.42317.670456.022722.3377
25.29810.19332.1397-0.26650.00270.894-0.15310.73510.178-0.27550.11110.225-0.03980.07240.05940.9959-0.3319-0.21240.76450.1530.8212-27.346248.12631.3003
32.7018-0.76381.26823.2187-1.31989.0208-0.2405-0.15660.0558-0.05110.19710.33810.26840.4128-0.07590.7898-0.0566-0.1890.5470.06770.7545-51.824942.508421.8435
44.9222-2.07893.26053.2128-2.12246.7644-0.155-0.4131-0.06150.43570.0949-0.03310.0388-0.03160.03210.85930.23950.04730.4727-0.0590.614-26.157936.541271.6901
58.1396-2.30665.55882.4857-2.37526.17470.29570.3559-1.289-0.59870.30980.38270.4292-0.5509-0.50621.3274-0.3053-0.13770.7164-0.0131.283-33.1362.39811.797
62.93811.4970.29893.6621-0.98720.9410.2982-0.2075-1.20580.5488-0.2607-1.00190.30110.1458-0.14280.8462-0.0059-0.01950.38710.02510.80276.771515.518734.8628
71.28740.2862-0.56934.6073-1.54022.790.09840.0834-0.8833-0.12560.157-0.81960.27550.4518-0.23550.691-0.0766-0.0120.4161-0.00941.062518.391727.144831.7473
83.84183.39520.07654.78990.85940.0008-0.0753-0.2195-0.50220.0282-0.0898-0.280.3084-0.09670.16670.9226-0.0438-0.01310.38130.07950.7074-3.833118.65133.7582
92.18-3.26911.68453.2293-2.70612.10990.68092.6311-0.2506-1.6997-0.64010.43641.30270.2625-0.01452.0135-0.3861-0.12962.032-0.07131.0894-30.5697.8594-2.3379
106.0040.25622.83392.6982.0843.5831-0.65970.7280.9211-0.9438-0.14951.0887-0.171-0.02590.80491.2157-0.2304-0.25020.86460.06571.3107-38.530124.407115.2156
114.3504-6.79944.58942.2259-6.56264.3707-0.1708-0.335-0.007-0.41410.2678-1.37930.1384-0.4051-0.16120.9494-0.0260.03840.5691-0.03821.0607-18.548217.32858.9574
123.2282.30510.87591.69691.94665.7685-0.0670.1901-0.070.14720.1623-0.70190.01350.6996-0.17421.32790.2755-0.04870.58090.08421.2316-7.549415.236268.4775
130.1995-0.4275-1.37641.18153.56861.99720.63490.46840.18020.8019-0.339-0.2921-0.21920.8305-0.12973.05410.6199-0.87021.8254-0.44012.123427.436947.189961.8913
140.55141.0101-0.12492.0306-0.3060.05020.0147-2.03551.38811.3349-1.56112.1458-1.51021.54511.28855.26851.3106-0.80644.1225-1.61952.730915.933146.435478.4304
159.2787-4.19878.90622.066-6.53892.0855-0.2749-1.80380.71751.9619-1.0808-1.11842.79970.85851.37042.3062-0.0045-0.03171.6258-0.12151.096818.644546.668860.1587
162.0047-1.54764.34227.5854.47419.3371-0.86022.18213.784-1.6325-1.8395-0.3513-2.61040.56922.54972.8450.3147-0.1911.79210.2552.397816.317828.873268.6822
176.658-6.7997-1.63077.60714.01538.55130.5768-1.3693-0.69122.2399-1.69172.71451.51241.72171.11221.9604-0.17820.47991.4019-0.02121.162713.278548.299662.6235
186.87844.408-0.67433.8529-3.45569.03280.4175-0.4821-0.0227-1.2215-1.4617-1.51834.04372.97251.10772.13610.47410.34133.05730.91161.962314.596336.336876.4496
196.0018-3.1645-5.80471.66283.04845.6361-0.1676-3.373-0.21992.73050.6362-1.07772.94590.4031-0.52293.0997-0.9451-0.06372.5867-0.36141.07519.630940.149961.7817
207.0362-5.0136-7.14674.76476.56569.1199-0.2013-1.86191.18582.088-0.4101-2.74863.65071.08010.43151.5795-0.1504-0.37930.74290.13591.219420.823541.561648.3461
21-0.0149-0.0151-0.0129-0.0195-0.0095-0.00541.8068-2.1859-0.11721.17080.30770.0987-5.36890.7216-1.84472.48790.14580.79883.61460.6441.681423.869238.868873.2168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 320 )
2X-RAY DIFFRACTION2chain 'A' and (resid 321 through 590 )
3X-RAY DIFFRACTION3chain 'A' and (resid 591 through 729 )
4X-RAY DIFFRACTION4chain 'A' and (resid 730 through 956 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 75 )
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 169 )
7X-RAY DIFFRACTION7chain 'B' and (resid 170 through 278 )
8X-RAY DIFFRACTION8chain 'B' and (resid 279 through 423 )
9X-RAY DIFFRACTION9chain 'B' and (resid 424 through 462 )
10X-RAY DIFFRACTION10chain 'B' and (resid 463 through 588 )
11X-RAY DIFFRACTION11chain 'B' and (resid 589 through 630 )
12X-RAY DIFFRACTION12chain 'B' and (resid 631 through 690 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1417 through 1425 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1426 through 1433 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1434 through 1452 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1453 through 1461 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1462 through 1473 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1474 through 1483 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1484 through 1490 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1491 through 1502 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1503 through 1509 )

+
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