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- PDB-7r85: Structure of mouse Bai1 (ADGRB1) TSR3 domain -

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Basic information

Entry
Database: PDB / ID: 7r85
TitleStructure of mouse Bai1 (ADGRB1) TSR3 domain
ComponentsVasculostatin-120
KeywordsCELL ADHESION / adhesion GPCR / O-linked glycosylation / C-mannosylation / thrombospondin type 1 repeat (TSR) domain
Function / homology
Function and homology information


postsynaptic actin cytoskeleton organization / engulfment of apoptotic cell / phagocytosis, recognition / positive regulation of synapse assembly / negative regulation of endothelial cell migration / muscle organ development / positive regulation of reactive oxygen species biosynthetic process / phagocytosis, engulfment / positive regulation of myoblast fusion / phosphatidylserine binding ...postsynaptic actin cytoskeleton organization / engulfment of apoptotic cell / phagocytosis, recognition / positive regulation of synapse assembly / negative regulation of endothelial cell migration / muscle organ development / positive regulation of reactive oxygen species biosynthetic process / phagocytosis, engulfment / positive regulation of myoblast fusion / phosphatidylserine binding / phagocytic cup / negative regulation of protein ubiquitination / negative regulation of angiogenesis / PDZ domain binding / G protein-coupled receptor activity / lipopolysaccharide binding / regulation of synaptic plasticity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of protein catabolic process / transmembrane signaling receptor activity / nervous system development / postsynaptic membrane / defense response to Gram-negative bacterium / dendritic spine / postsynaptic density / cell surface receptor signaling pathway / innate immune response / focal adhesion / glutamatergic synapse / dendrite / perinuclear region of cytoplasm / extracellular space / plasma membrane
Similarity search - Function
Adhesion G protein-coupled receptor B, N-terminal domain / Adhesion GPCR B N-terminal region / GPCR, family 2, brain-specific angiogenesis inhibitor / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain ...Adhesion G protein-coupled receptor B, N-terminal domain / Adhesion GPCR B N-terminal region / GPCR, family 2, brain-specific angiogenesis inhibitor / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2.
Similarity search - Domain/homology
alpha-D-mannopyranose / Adhesion G protein-coupled receptor B1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMiao, Y. / Jude, K.M. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2021
Title: RTN4/NoGo-receptor binding to BAI adhesion-GPCRs regulates neuronal development.
Authors: Wang, J. / Miao, Y. / Wicklein, R. / Sun, Z. / Wang, J. / Jude, K.M. / Fernandes, R.A. / Merrill, S.A. / Wernig, M. / Garcia, K.C. / Sudhof, T.C.
History
DepositionJun 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vasculostatin-120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7674
Polymers6,0811
Non-polymers6873
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.915, 43.915, 64.312
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

21A-328-

HOH

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Components

#1: Protein Vasculostatin-120 / Vstat120


Mass: 6080.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adgrb1, Bai1 / Production host: Homo sapiens (human) / Strain (production host): h / References: UniProt: Q3UHD1
#2: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3LFucpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Fucp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1 M succinic acid, 0.1 M HEPES, pH 7.0 and 1% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.45→43.92 Å / Num. obs: 11734 / % possible obs: 99.9 % / Redundancy: 12.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.019 / Rrim(I) all: 0.063 / Net I/σ(I): 15 / Num. measured all: 142182 / Scaling rejects: 44
Reflection shell

Diffraction-ID: 1 / % possible all: 99.4

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.45-1.4710.93.88161945700.671.2214.0750.6
7.94-43.9290.0439171020.9990.0160.04637.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: complex structure of BAI1-RTN4R

Resolution: 1.45→43.915 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 1171 10.02 %
Rwork0.1785 10517 -
obs0.1817 11688 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.8 Å2 / Biso mean: 43.3293 Å2 / Biso min: 24.3 Å2
Refinement stepCycle: final / Resolution: 1.45→43.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms352 0 43 43 438
Biso mean--53.47 47.85 -
Num. residues----44
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.45-1.5160.36641420.3147127298
1.516-1.59590.25781410.2206126299
1.5959-1.69590.24331440.18411295100
1.6959-1.82680.23791440.16161294100
1.8268-2.01070.19341450.13171304100
2.0107-2.30160.1851460.14531320100
2.3016-2.89970.22361490.18971335100
2.8997-43.9150.20561600.1843143599

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