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- PDB-6gff: Structure of GARP (LRRC32) in complex with latent TGF-beta1 and M... -

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Basic information

Entry
Database: PDB / ID: 6gff
TitleStructure of GARP (LRRC32) in complex with latent TGF-beta1 and MHG-8 Fab
Components
  • (Transforming growth factor beta- ...) x 2
  • Leucine-rich repeat-containing protein 32
  • MHG-8 Fab heavy chain
  • MHG-8 Fab light chain
KeywordsIMMUNE SYSTEM / GARP / TGF-B1 / Activation / Treg
Function / homology
Function and homology information


: / positive regulation of primary miRNA processing / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / TGFBR2 MSI Frameshift Mutants in Cancer / regulatory T cell differentiation / regulation of blood vessel remodeling / regulation of striated muscle tissue development / extracellular matrix assembly ...: / positive regulation of primary miRNA processing / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / TGFBR2 MSI Frameshift Mutants in Cancer / regulatory T cell differentiation / regulation of blood vessel remodeling / regulation of striated muscle tissue development / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / regulation of protein import into nucleus / embryonic liver development / type III transforming growth factor beta receptor binding / negative regulation of hyaluronan biosynthetic process / positive regulation of cardiac muscle cell differentiation / myofibroblast differentiation / odontoblast differentiation / connective tissue replacement involved in inflammatory response wound healing / positive regulation of receptor signaling pathway via STAT / negative regulation of macrophage cytokine production / TGFBR2 Kinase Domain Mutants in Cancer / : / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / secondary palate development / membrane protein intracellular domain proteolysis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / heart valve morphogenesis / positive regulation of vasculature development / hyaluronan catabolic process / regulation of transforming growth factor beta receptor signaling pathway / ATP biosynthetic process / receptor catabolic process / positive regulation of extracellular matrix assembly / negative regulation of extracellular matrix disassembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / positive regulation of chemotaxis / type I transforming growth factor beta receptor binding / negative regulation of biomineral tissue development / cell-cell junction organization / negative regulation of myoblast differentiation / positive regulation of vascular permeability / deubiquitinase activator activity / transforming growth factor beta binding / positive regulation of endothelial cell apoptotic process / response to cholesterol / positive regulation of chemokine (C-X-C motif) ligand 2 production / aortic valve morphogenesis / positive regulation of fibroblast migration / phosphate-containing compound metabolic process / negative regulation of protein localization to plasma membrane / sprouting angiogenesis / neural tube development / Molecules associated with elastic fibres / RUNX3 regulates CDKN1A transcription / negative regulation of cytokine production / positive regulation of epidermal growth factor receptor signaling pathway / ventricular cardiac muscle tissue morphogenesis / negative regulation of fat cell differentiation / macrophage derived foam cell differentiation / Syndecan interactions / negative regulation of cell-cell adhesion / positive regulation of interleukin-17 production / negative regulation of blood vessel endothelial cell migration / TGF-beta receptor signaling activates SMADs / negative regulation of activated T cell proliferation / plasma membrane => GO:0005886 / negative regulation of cell differentiation / positive regulation of SMAD protein signal transduction / RUNX3 regulates p14-ARF / positive regulation of cell division / cellular response to low-density lipoprotein particle stimulus / negative regulation of cell cycle / ECM proteoglycans / positive regulation of vascular endothelial growth factor production / epithelial to mesenchymal transition / positive regulation of collagen biosynthetic process / positive regulation of epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / lymph node development / vasculogenesis / chondrocyte differentiation / hematopoietic progenitor cell differentiation / salivary gland morphogenesis / regulation of cell migration / extrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / cellular response to transforming growth factor beta stimulus / antigen binding / extracellular matrix / positive regulation of protein metabolic process / protein export from nucleus / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / positive regulation of superoxide anion generation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / negative regulation of miRNA transcription
Similarity search - Function
Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / Leucine rich repeat N-terminal domain / 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 / Leucine-rich repeat N-terminal domain ...Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / Leucine rich repeat N-terminal domain / 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 / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transforming growth factor beta-1 proprotein / Transforming growth factor beta activator LRRC32
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMerceron, R. / Lienart, S. / Vanderaa, C. / Colau, D. / Stockis, J. / Van Der Woning, B. / De Haard, H. / Saunders, M. / Coulie, P.G. / Savvides, S.N. / Lucas, S.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Walloon Excellence in Lifesciences & BIOtechnologyBF-2014-01 Belgium
European Research CouncilTARG-SUP 682818 Belgium
CitationJournal: Science / Year: 2018
Title: Structural basis of latent TGF-beta 1 presentation and activation by GARP on human regulatory T cells.
Authors: Lienart, S. / Merceron, R. / Vanderaa, C. / Lambert, F. / Colau, D. / Stockis, J. / van der Woning, B. / De Haard, H. / Saunders, M. / Coulie, P.G. / Savvides, S.N. / Lucas, S.
History
DepositionApr 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming growth factor beta-1
B: Transforming growth factor beta-1
C: Transforming growth factor beta-1
D: Transforming growth factor beta-1
E: Transforming growth factor beta-1
F: Transforming growth factor beta-1
G: Transforming growth factor beta-1
H: Transforming growth factor beta-1
I: Leucine-rich repeat-containing protein 32
J: Leucine-rich repeat-containing protein 32
K: MHG-8 Fab light chain
L: MHG-8 Fab heavy chain
M: MHG-8 Fab light chain
N: MHG-8 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)398,36121
Polymers394,25514
Non-polymers4,1067
Water0
1
A: Transforming growth factor beta-1
B: Transforming growth factor beta-1
C: Transforming growth factor beta-1
D: Transforming growth factor beta-1
I: Leucine-rich repeat-containing protein 32
K: MHG-8 Fab light chain
L: MHG-8 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,31211
Polymers197,1287
Non-polymers2,1844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Transforming growth factor beta-1
F: Transforming growth factor beta-1
G: Transforming growth factor beta-1
H: Transforming growth factor beta-1
J: Leucine-rich repeat-containing protein 32
M: MHG-8 Fab light chain
N: MHG-8 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,04910
Polymers197,1287
Non-polymers1,9223
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.860, 175.010, 145.770
Angle α, β, γ (deg.)90.00, 92.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Transforming growth factor beta- ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
Transforming growth factor beta-1 / / TGF-beta-1


Mass: 28531.488 Da / Num. of mol.: 4 / Fragment: LAP
Source method: isolated from a genetically manipulated source
Details: Mature protein expected to start at Leucine30. Obtained after cleavage of Pro-TGF-b1 by Furin after Arginine278.
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Production host: Homo sapiens (human) / References: UniProt: P01137
#2: Protein
Transforming growth factor beta-1 / / TGF-beta-1


Mass: 12809.812 Da / Num. of mol.: 4 / Fragment: Mature
Source method: isolated from a genetically manipulated source
Details: Obtained after cleavage of Pro-TGF-b1 by Furin after Arginine278.
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Production host: Homo sapiens (human) / References: UniProt: P01137

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Protein , 1 types, 2 molecules IJ

#3: Protein Leucine-rich repeat-containing protein 32 / Garpin / Glycoprotein A repetitions predominant / GARP


Mass: 67235.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Mature protein expected to start at Histidine20. / Source: (gene. exp.) Homo sapiens (human) / Gene: LRRC32, D11S833E, GARP / Production host: Homo sapiens (human) / References: UniProt: Q14392

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Antibody , 2 types, 4 molecules KMLN

#4: Antibody MHG-8 Fab light chain


Mass: 23376.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Mature protein expected to start at Aspartic acid21.
Source: (natural) Mus musculus (house mouse)
#5: Antibody MHG-8 Fab heavy chain


Mass: 23832.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Mature protein expected to start at Glutamine20. / Source: (natural) Mus musculus (house mouse)

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Sugars , 3 types, 7 molecules

#6: 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.: 5
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
#7: 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-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
#8: 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.: 1
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

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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: 62.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 15% (w/v) PEG4000, 0.1 M HEPES pH 6.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 84967 / % possible obs: 90.1 % / Redundancy: 2.3 % / Biso Wilson estimate: 77.7 Å2 / Net I/σ(I): 8.15
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 2.2 % / Num. unique obs: 6320 / % possible all: 90.6

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Processing

Software
NameClassification
PHENIXrefinement
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→29.921 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.07
RfactorNum. reflection% reflection
Rfree0.2684 4244 5 %
Rwork0.233 --
obs0.2348 84892 90.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→29.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21395 0 273 0 21668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222185
X-RAY DIFFRACTIONf_angle_d0.54830416
X-RAY DIFFRACTIONf_dihedral_angle_d8.7313321
X-RAY DIFFRACTIONf_chiral_restr0.0413608
X-RAY DIFFRACTIONf_plane_restr0.0033925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0999-3.13510.37641430.33682706X-RAY DIFFRACTION90
3.1351-3.17190.39681420.33442698X-RAY DIFFRACTION91
3.1719-3.21060.4081370.33542621X-RAY DIFFRACTION88
3.2106-3.25120.34271310.32522485X-RAY DIFFRACTION83
3.2512-3.29390.40561300.32132453X-RAY DIFFRACTION83
3.2939-3.3390.36721480.3212821X-RAY DIFFRACTION95
3.339-3.38660.33911490.30372817X-RAY DIFFRACTION94
3.3866-3.43710.34721460.28342796X-RAY DIFFRACTION94
3.4371-3.49070.30661470.26722797X-RAY DIFFRACTION94
3.4907-3.54790.3141450.26692770X-RAY DIFFRACTION93
3.5479-3.60890.29591460.26442770X-RAY DIFFRACTION93
3.6089-3.67440.29371460.25032777X-RAY DIFFRACTION93
3.6744-3.7450.34071460.24812773X-RAY DIFFRACTION93
3.745-3.82130.27221460.24292772X-RAY DIFFRACTION93
3.8213-3.90420.24651440.21672741X-RAY DIFFRACTION93
3.9042-3.99480.23661460.20642774X-RAY DIFFRACTION92
3.9948-4.09450.23231440.20432726X-RAY DIFFRACTION93
4.0945-4.20490.23891430.20222723X-RAY DIFFRACTION91
4.2049-4.32830.21271420.19462687X-RAY DIFFRACTION90
4.3283-4.46750.23441400.18682669X-RAY DIFFRACTION90
4.4675-4.62670.20361370.18712608X-RAY DIFFRACTION88
4.6267-4.81120.19971250.17812366X-RAY DIFFRACTION80
4.8112-5.02920.20221420.18752689X-RAY DIFFRACTION90
5.0292-5.29290.23891440.19942742X-RAY DIFFRACTION92
5.2929-5.62250.2691430.20862724X-RAY DIFFRACTION91
5.6225-6.05330.26271430.23822720X-RAY DIFFRACTION90
6.0533-6.65640.29581420.25412692X-RAY DIFFRACTION90
6.6564-7.60580.3111390.25472649X-RAY DIFFRACTION88
7.6058-9.53080.25111290.23222442X-RAY DIFFRACTION81
9.5308-29.92260.26961390.24462640X-RAY DIFFRACTION86
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)
10.9450.60.08634.39151.33052.39540.19810.2013-0.7466-0.76340.12290.56630.9794-0.4536-0.29011.2979-0.0617-0.4880.8509-0.01091.11086.283529.044313.504
23.5815-0.53390.40173.16061.00262.2338-0.03060.2515-0.3654-0.48180.1562-0.11090.33970.5727-0.19120.4975-0.0413-0.06170.4640.01230.513224.835648.065129.2051
33.27510.47490.12476.41860.20763.1649-0.0376-0.239-1.07630.53120.13710.18351.19960.2266-0.03910.83680.0937-0.1150.69550.12120.776818.004934.394346.895
43.88272.1244.33534.09414.48499.6043-0.07130.2495-0.2485-0.5374-0.15430.84250.5474-0.85810.32050.72-0.1771-0.22260.69320.02050.66795.134349.333820.5
51.6462-2.33230.27615.6571-0.60362.1535-0.3024-0.30680.1290.84670.422-0.56040.27860.6382-0.14020.74610.1028-0.16090.8176-0.18320.519848.642129.5933-5.1536
63.7058-0.06661.25744.36811.96116.94690.2434-0.0152-0.03810.16050.05310.42340.3453-0.4241-0.30050.41610.0691-0.05960.30910.03530.494824.847440.1507-26.8089
74.0928-3.3141.4725.897-2.05871.2470.41870.434-0.4763-0.8014-0.3319-0.0150.60790.2518-0.10030.75350.0761-0.10020.6112-0.13440.387939.990123.5913-37.4498
85.7553-1.35966.76322.1029-1.6979.5065-0.0915-0.15490.38390.3064-0.0263-0.11-0.2620.44420.08490.53790.0262-0.01230.4784-0.08130.403840.295951.8687-16.9264
93.542-0.148-2.40870.65470.00052.88980.08570.23840.2826-0.0280.0844-0.0494-0.3792-0.0395-0.18620.5993-0.0775-0.13760.31420.02630.451632.794678.205226.5735
101.60790.3354-0.72681.1131-1.09534.01930.14520.00730.24060.11460.1770.4092-0.4622-0.5667-0.31780.55570.1773-0.06440.46390.04960.62098.929664.6117-34.3796
113.31010.9753-1.01561.2392-0.54991.52740.0260.69740.6460.20760.35770.9094-0.1008-1.3033-0.38620.61240.1940.06591.66360.08821.0345-31.098665.711860.3335
129.45440.8371-1.5050.78650.30460.8475-0.05910.3277-0.51370.0314-0.08170.53480.3745-1.52040.1120.66-0.1781-0.08311.69110.06470.8441-25.079452.180651.6456
138.8672.5765-3.37086.4742-1.564.498-0.77851.25082.2658-0.50740.397-0.2016-1.38631.19360.23830.9376-0.4348-0.24941.26260.41011.10354.841377.3454-51.7978
142.17971.1051-1.10256.50170.16423.57160.2963-0.1036-0.00290.1957-0.3015-0.68820.18521.8446-0.0180.6083-0.0309-0.12881.43230.12590.616257.263458.1868-44.8236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 30 through 266)
2X-RAY DIFFRACTION2(chain 'B' and resid 279 through 390)
3X-RAY DIFFRACTION3(chain 'C' and resid 32 through 274)
4X-RAY DIFFRACTION4(chain 'D' and resid 280 through 390)
5X-RAY DIFFRACTION5(chain 'E' and resid 30 through 269)
6X-RAY DIFFRACTION6(chain 'F' and resid 279 through 390)
7X-RAY DIFFRACTION7(chain 'G' and resid 32 through 270)
8X-RAY DIFFRACTION8(chain 'H' and resid 282 through 390)
9X-RAY DIFFRACTION9(chain 'I' and resid 20 through 591)
10X-RAY DIFFRACTION10(chain 'J' and resid 20 through 546)
11X-RAY DIFFRACTION11(chain 'K' and resid 21 through 232)
12X-RAY DIFFRACTION12(chain 'L' and resid 20 through 240)
13X-RAY DIFFRACTION13(chain 'M' and resid 21 through 124)
14X-RAY DIFFRACTION14(chain 'N' and resid 20 through 137)

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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

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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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