[English] 日本語
Yorodumi
- PDB-5ffo: Integrin alpha V beta 6 in complex with pro-TGF-beta -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ffo
TitleIntegrin alpha V beta 6 in complex with pro-TGF-beta
Components
  • Integrin alpha-V
  • Integrin beta-6
  • Transforming growth factor beta-1
KeywordsCELL ADHESION / Integrin / TGF-beta
Function / homology
Function and homology information


cellular response to acetaldehyde / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / positive regulation of microglia differentiation / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / Influenza Virus Induced Apoptosis / regulation of branching involved in mammary gland duct morphogenesis / negative regulation of skeletal muscle tissue development / macrophage derived foam cell differentiation ...cellular response to acetaldehyde / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / positive regulation of microglia differentiation / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / Influenza Virus Induced Apoptosis / regulation of branching involved in mammary gland duct morphogenesis / negative regulation of skeletal muscle tissue development / macrophage derived foam cell differentiation / frontal suture morphogenesis / regulation of enamel mineralization / regulation of cartilage development / TGFBR2 MSI Frameshift Mutants in Cancer / regulation of striated muscle tissue development / regulatory T cell differentiation / tolerance induction to self antigen / regulation of blood vessel remodeling / regulation of protein import into nucleus / embryonic liver development / extracellular matrix assembly / columnar/cuboidal epithelial cell maturation / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of hyaluronan biosynthetic process / type III transforming growth factor beta receptor binding / positive regulation of cardiac muscle cell differentiation / myofibroblast differentiation / odontoblast differentiation / connective tissue replacement involved in inflammatory response wound healing / hard palate development / positive regulation of odontogenesis / Langerhans cell differentiation / negative regulation of macrophage cytokine production / positive regulation of exit from mitosis / positive regulation of smooth muscle cell differentiation / TGFBR2 Kinase Domain Mutants in Cancer / 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 / positive regulation of isotype switching to IgA isotypes / extracellular matrix protein binding / opsonin binding / positive regulation of mesenchymal stem cell proliferation / enamel mineralization / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / mammary gland branching involved in thelarche / positive regulation of receptor signaling pathway via STAT / membrane protein intracellular domain proteolysis / retina vasculature development in camera-type eye / heart valve morphogenesis / integrin alphav-beta1 complex / TGFBR3 regulates TGF-beta signaling / bronchiole development / Cross-presentation of particulate exogenous antigens (phagosomes) / response to laminar fluid shear stress / hyaluronan catabolic process / positive regulation of vasculature development / lens fiber cell differentiation / positive regulation of extracellular matrix assembly / ATP biosynthetic process / receptor catabolic process / negative regulation of extracellular matrix disassembly / Laminin interactions / positive regulation of branching involved in ureteric bud morphogenesis / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / negative regulation of biomineral tissue development / response to salt / oligodendrocyte development / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / type I transforming growth factor beta receptor binding / germ cell migration / entry into host cell by a symbiont-containing vacuole / positive regulation of mononuclear cell migration / alphav-beta3 integrin-PKCalpha complex / positive regulation of chemotaxis / endoderm development / phospholipid homeostasis / alphav-beta3 integrin-HMGB1 complex / negative regulation of myoblast differentiation / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of lipid transport / cell-cell junction organization / response to vitamin D / regulation of phagocytosis / : / response to cholesterol / positive regulation of vascular permeability / Elastic fibre formation / negative regulation of interleukin-17 production / surfactant homeostasis / alphav-beta3 integrin-IGF-1-IGF1R complex / deubiquitinase activator activity / transforming growth factor beta binding / negative regulation of release of sequestered calcium ion into cytosol / positive regulation of chemokine (C-X-C motif) ligand 2 production
Similarity search - Function
Jelly Rolls - #970 / Transforming growth factor beta-1 proprotein / Integrin domains. Chain A, domain 2 / Transforming growth factor-beta / Integrin alpha, N-terminal / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related ...Jelly Rolls - #970 / Transforming growth factor beta-1 proprotein / Integrin domains. Chain A, domain 2 / Transforming growth factor-beta / Integrin alpha, N-terminal / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / 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 beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / 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) / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / 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 / Cystine-knot cytokine / 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. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Jelly Rolls / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Transforming growth factor beta-1 proprotein / Integrin alpha-V / Integrin beta-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.49 Å
AuthorsDong, X. / Zhao, B. / Springer, T.A.
CitationJournal: Nature / Year: 2017
Title: Force interacts with macromolecular structure in activation of TGF-beta.
Authors: Dong, X. / Zhao, B. / Iacob, R.E. / Zhu, J. / Koksal, A.C. / Lu, C. / Engen, J.R. / Springer, T.A.
History
DepositionDec 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / 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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _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_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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-V
B: Integrin beta-6
C: Transforming growth factor beta-1
D: Transforming growth factor beta-1
E: Integrin alpha-V
F: Integrin beta-6
G: Transforming growth factor beta-1
H: Transforming growth factor beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,61640
Polymers355,6278
Non-polymers12,98932
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34200 Å2
ΔGint75 kcal/mol
Surface area138500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.440, 91.440, 131.030
Angle α, β, γ (deg.)89.98, 86.25, 89.85
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 3 types, 8 molecules AEBFCDGH

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


Mass: 65982.922 Da / Num. of mol.: 2 / Fragment: UNP residues 31-627
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA / Production host: Homo sapiens (human) / References: UniProt: P06756
#2: Protein Integrin beta-6


Mass: 28851.707 Da / Num. of mol.: 2 / Fragment: Unp residues 128-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB6 / Production host: Homo sapiens (human) / References: UniProt: P18564
#3: Protein
Transforming growth factor beta-1 / TGF-beta-1


Mass: 41489.371 Da / Num. of mol.: 4 / Fragment: UNP residues 34-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Production host: Homo sapiens (human) / References: UniProt: P01137

-
Sugars , 8 types, 18 molecules

#4: 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
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[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]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-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)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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.: 2
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
#9: 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.: 3
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
#10: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]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]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#12: 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.: 4
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 , 3 types, 19 molecules

#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#13: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8% PEG8000 0.1M Immidazole / PH range: 7.5-8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 3.49→50 Å / Num. obs: 45279 / % possible obs: 94.6 % / Redundancy: 1.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.168 / Net I/σ(I): 4.6
Reflection shellResolution: 3.5→3.64 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.4 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 3.49→45.72 Å / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.95 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2774 1116 2.46 %
Rwork0.2236 --
obs0.2257 45279 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.49→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22945 0 836 5 23786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724469
X-RAY DIFFRACTIONf_angle_d0.79833145
X-RAY DIFFRACTIONf_dihedral_angle_d11.43514775
X-RAY DIFFRACTIONf_chiral_restr0.0453786
X-RAY DIFFRACTIONf_plane_restr0.0044184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4948-3.65350.30781390.28145647X-RAY DIFFRACTION95
3.6535-3.84560.29441290.28325610X-RAY DIFFRACTION94
3.8456-4.08590.29051350.28895609X-RAY DIFFRACTION94
4.0859-4.40020.35651470.28095430X-RAY DIFFRACTION92
4.4002-4.84080.30771200.25045551X-RAY DIFFRACTION93
4.8408-5.53640.26111380.22585496X-RAY DIFFRACTION93
5.5364-6.95680.31551240.21325485X-RAY DIFFRACTION92
6.9568-27.62760.23281260.16685273X-RAY DIFFRACTION89
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)
13.20781.23070.63883.4324-1.14184.6346-0.0145-0.22480.5827-0.4781-0.3381-0.87170.45231.8850.32910.84140.8803-0.13772.4760.24412.60285.891-12.773428.0881
20.6045-0.14431.93010.534-0.16676.05720.0497-0.00960.73530.8469-0.3804-0.3132-0.12471.61320.43492.0681-0.0538-0.58933.0336-0.46822.346220.9843-13.421478.5475
32.5677-1.6587-0.52978.59371.51088.18641.79930.22.4533-2.4543-1.50294.3965-0.5156-0.9771-0.50620.8671-0.1914-0.58521.03410.41612.338-25.912-1.121723.2451
45.9439-3.39550.42335.1988-3.07223.59530.82110.8581-0.7611-2.0155-0.62250.33151.18670.3923-0.24892.29820.0296-0.1131.7862-0.42931.4506-21.6655-17.3987-46.163
51.78440.8997-2.88151.07070.30549.66690.17120.89890.7853-1.15740.39190.21330.3524-1.4933-0.50812.49770.5953-0.3392.1728-0.0941.929-44.76785.3811-48.5697
66.8323-0.5789-2.82683.21430.31485.6067-0.18460.7337-1.74870.2339-0.20440.03990.29780.93980.3871.73380.3236-0.56481.5444-0.20471.6575-29.3088-14.6847-11.8844
73.54552.8342-5.02547.7608-3.43338.26370.7824-0.24650.8045-0.4917-0.11170.37870.01780.8212-0.49421.95091.1581-0.47212.2985-0.39481.5946-40.819813.0102-19.7696
84.14121.0825-0.72980.55750.60417.1412-0.00540.42920.7251-0.132-0.48970.8695-0.9027-1.80920.38371.83950.7612-0.1441.5728-0.24721.7493-6.3688-58.3939-26.871
94.1476-1.23750.76172.8021-1.7182.621-0.29571.23760.2808-0.45110.29090.38820.5943-0.465-0.1132.10840.3535-0.34682.8865-0.12422.3933-21.4691-58.958-76.9923
109.8717-2.0624-2.18765.3751.28584.4994-1.07490.8798-0.6311-0.50521.08761.8643-0.8674-1.11270.16682.1365-0.0354-0.57441.52350.17072.557825.6069-46.8526-21.9897
117.48790.2011-0.02675.9341-0.41526.06150.1442-1.6511-1.45071.56610.35250.55340.876-0.5787-0.36081.99730.07130.23151.82320.44011.512721.3391-63.136747.3858
122.92483.2482-3.51963.8854-5.13219.14620.8315-1.1154-0.2951.5704-1.7243-0.7349-2.61680.82010.71942.64710.2881-0.30562.01240.02691.603944.0283-40.199549.8581
136.88792.49171.78283.1124-1.4032.3240.06510.8059-0.37750.10250.2079-0.09840.397-0.2333-0.28182.09720.29030.32021.4558-0.29161.250428.6073-60.797513.4684
144.76781.96190.54531.7955-2.25926.4019-1.02730.1765-1.15340.5810.01590.14320.54040.77281.14291.74120.6372-0.27670.6167-0.49272.45840.5503-32.415720.6862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:438 )A1 - 438
2X-RAY DIFFRACTION2( CHAIN A AND RESID 439:594 )A439 - 594
3X-RAY DIFFRACTION3( CHAIN B AND ( RESID 113:354 OR RESID 2001:2004 ) )B113 - 354
4X-RAY DIFFRACTION3( CHAIN B AND ( RESID 113:354 OR RESID 2001:2004 ) )B2001 - 2004
5X-RAY DIFFRACTION4( CHAIN C AND RESID 42:240 )C42 - 240
6X-RAY DIFFRACTION5( CHAIN C AND ( RESID 8:41 OR RESID 250:361 ) )C8 - 41
7X-RAY DIFFRACTION5( CHAIN C AND ( RESID 8:41 OR RESID 250:361 ) )C250 - 361
8X-RAY DIFFRACTION6( CHAIN D AND RESID 42:240 )D42 - 240
9X-RAY DIFFRACTION7( CHAIN D AND ( RESID 7:41 OR RESID 256:361 ) )D7 - 41
10X-RAY DIFFRACTION7( CHAIN D AND ( RESID 7:41 OR RESID 256:361 ) )D256 - 361
11X-RAY DIFFRACTION8( CHAIN E AND RESID 1:438 )E1 - 438
12X-RAY DIFFRACTION9( CHAIN E AND RESID 439:591 )E439 - 591
13X-RAY DIFFRACTION10( CHAIN F AND ( RESID 113:354 OR RESID 2001:2004 ) )F113 - 354
14X-RAY DIFFRACTION10( CHAIN F AND ( RESID 113:354 OR RESID 2001:2004 ) )F2001 - 2004
15X-RAY DIFFRACTION11( CHAIN G AND RESID 42:240 )G42 - 240
16X-RAY DIFFRACTION12( CHAIN G AND ( RESID 10:41 OR RESID 250:361 ) )G10 - 41
17X-RAY DIFFRACTION12( CHAIN G AND ( RESID 10:41 OR RESID 250:361 ) )G250 - 361
18X-RAY DIFFRACTION13( CHAIN H AND RESID 42:240 )H42 - 240
19X-RAY DIFFRACTION14( CHAIN H AND ( RESID 5:41 OR RESID 259:361 ) )H5 - 41
20X-RAY DIFFRACTION14( CHAIN H AND ( RESID 5:41 OR RESID 259:361 ) )H259 - 361

+
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