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- PDB-5kvm: Extracellular region of mouse GPR56/ADGRG1 in complex with FN3 mo... -

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Basic information

Entry
Database: PDB / ID: 5kvm
TitleExtracellular region of mouse GPR56/ADGRG1 in complex with FN3 monobody
Components
  • (Adhesion G-protein coupled receptor ...) x 2
  • FN3 monobody alpha5
KeywordsCELL ADHESION / adhesion-GPCR / monobody / PLL / GAIN
Function / homology
Function and homology information


cerebral cortex regionalization / cerebral cortex radial glia-guided migration / glial limiting end-foot / negative regulation of neuron migration / hematopoietic stem cell homeostasis / layer formation in cerebral cortex / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of neural precursor cell proliferation / extracellular matrix binding / neural precursor cell proliferation ...cerebral cortex regionalization / cerebral cortex radial glia-guided migration / glial limiting end-foot / negative regulation of neuron migration / hematopoietic stem cell homeostasis / layer formation in cerebral cortex / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of neural precursor cell proliferation / extracellular matrix binding / neural precursor cell proliferation / positive regulation of Rho protein signal transduction / seminiferous tubule development / Rho protein signal transduction / collagen binding / positive regulation of cell adhesion / G protein-coupled receptor activity / cell migration / heparin binding / phospholipase C-activating G protein-coupled receptor signaling pathway / angiogenesis / cell surface receptor signaling pathway / cell adhesion / membrane raft / negative regulation of cell population proliferation / extracellular region / plasma membrane
Similarity search - Function
PTX/LNS-Like (PLL) domain / GPCR-Autoproteolysis-INducing (GAIN) subdomain A / PTX/LNS-Like (PLL) domain / GPCR-Autoproteolysis-INducing (GAIN) subdomain A / GPCR, family 2, orphan receptor, GPR1/GPR3/GPR5 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain ...PTX/LNS-Like (PLL) domain / GPCR-Autoproteolysis-INducing (GAIN) subdomain A / PTX/LNS-Like (PLL) domain / GPCR-Autoproteolysis-INducing (GAIN) subdomain A / GPCR, family 2, orphan receptor, GPR1/GPR3/GPR5 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Adhesion G-protein coupled receptor G1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.449 Å
AuthorsSalzman, G.S. / Ding, C. / Koide, S. / Arac, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F30-GM116455 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM087519 United States
Brain Research Foundation United States
CitationJournal: Neuron / Year: 2016
Title: Structural Basis for Regulation of GPR56/ADGRG1 by Its Alternatively Spliced Extracellular Domains.
Authors: Salzman, G.S. / Ackerman, S.D. / Ding, C. / Koide, A. / Leon, K. / Luo, R. / Stoveken, H.M. / Fernandez, C.G. / Tall, G.G. / Piao, X. / Monk, K.R. / Koide, S. / Arac, D.
History
DepositionJul 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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.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 / _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
Revision 2.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adhesion G-protein coupled receptor G1
B: Adhesion G-protein coupled receptor G1
C: FN3 monobody alpha5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2377
Polymers51,7513
Non-polymers1,4864
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-7 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.336, 120.336, 72.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Adhesion G-protein coupled receptor ... , 2 types, 2 molecules AB

#1: Protein Adhesion G-protein coupled receptor G1 / G-protein coupled receptor 56 / Serpentine receptor cyt28


Mass: 40330.262 Da / Num. of mol.: 1 / Fragment: N-terminal Fragment (UNP residues 28-382)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adgrg1, Cyt28, Gpr56 / Cell (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8K209
#2: Protein/peptide Adhesion G-protein coupled receptor G1 / G-protein coupled receptor 56 / Serpentine receptor cyt28


Mass: 1030.237 Da / Num. of mol.: 1 / Fragment: C-terminal fragment (UNP residues 383-391)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adgrg1, Cyt28, Gpr56 / Cell (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8K209

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Protein , 1 types, 1 molecules C

#3: Protein FN3 monobody alpha5


Mass: 10390.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Sugars , 3 types, 3 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-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
DManpb1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/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)][b-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.: 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
#6: 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.: 1
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

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Non-polymers , 2 types, 25 molecules

#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 80 mM sodium acetate pH 4.6, 19.5% glycerol, 16.9% PEG 600, 7.6% PEG 1000

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.449→46.391 Å / Num. obs: 22286 / % possible obs: 99.9 % / Redundancy: 5.7 % / CC1/2: 0.923 / Rmerge(I) obs: 0.035 / Net I/σ(I): 19.75
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.663 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.449→46.391 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 1162 5.22 %
Rwork0.2146 --
obs0.2171 22242 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.449→46.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 98 24 3698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033783
X-RAY DIFFRACTIONf_angle_d0.6115182
X-RAY DIFFRACTIONf_dihedral_angle_d13.3152237
X-RAY DIFFRACTIONf_chiral_restr0.043601
X-RAY DIFFRACTIONf_plane_restr0.004656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4488-2.56020.34631440.29272617X-RAY DIFFRACTION99
2.5602-2.69520.30911400.2742617X-RAY DIFFRACTION100
2.6952-2.8640.33971440.25422629X-RAY DIFFRACTION100
2.864-3.08510.32671480.25012602X-RAY DIFFRACTION100
3.0851-3.39550.27921450.22422624X-RAY DIFFRACTION100
3.3955-3.88660.28341360.22252659X-RAY DIFFRACTION100
3.8866-4.89580.2411620.18382624X-RAY DIFFRACTION100
4.8958-46.39940.22211430.19822708X-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)
17.0355-0.7876-1.10514.72090.92044.5864-0.03730.6548-0.05040.1365-0.07290.3793-0.0629-0.90450.04850.68850.2151-0.00550.66840.00830.555935.012617.392719.4839
22.5490.14980.54132.45031.20375.4765-0.10290.32140.2804-0.4666-0.33310.363-1.09-0.7760.21650.92740.3188-0.19370.4696-0.08540.539650.674812.5054-15.9711
35.9618-0.1495-2.3023.5443-0.85127.04650.4870.565-0.2391-0.5418-0.2884-0.1913-1.7588-0.1374-0.06251.22210.2346-0.22580.5103-0.04780.670355.772215.4427-24.681
44.76-4.61581.77024.95590.03377.2750.58550.34760.2598-2.09440.83790.64150.3367-0.1174-0.11670.9129-0.09230.09790.73480.65880.906471.51857.270711.6813
54.08520.4313-2.72135.674-3.42676.1394-0.1665-0.48880.12520.4259-0.13230.063-1.07420.61290.28970.9115-0.0586-0.12610.3851-0.00940.485367.872512.299720.3869
65.1246-0.4077-0.53431.5763-0.99470.8735-0.3351-0.2492-0.8920.42970.33970.1122-1.2428-0.3034-0.06890.99640.0716-0.03390.3448-0.09480.586555.125211.880820.8186
75.24380.311-3.21231.5331-1.8795.91180.1512-0.5726-0.36360.6312-0.09340.0166-0.590.6674-0.02830.92930.0023-0.00620.3492-0.02630.510263.558910.993623.5303
81.2092-0.746-0.14013.02810.15360.2069-0.0963-0.0016-0.06040.3238-0.26690.0373-1.2850.02640.20070.7636-0.0229-0.0720.235-0.03830.498263.77910.954610.4944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 175 )
2X-RAY DIFFRACTION2chain 'A' and (resid 176 through 382 )
3X-RAY DIFFRACTION3chain 'B' and (resid 383 through 391 )
4X-RAY DIFFRACTION4chain 'C' and (resid 5 through 9 )
5X-RAY DIFFRACTION5chain 'C' and (resid 10 through 40 )
6X-RAY DIFFRACTION6chain 'C' and (resid 41 through 54 )
7X-RAY DIFFRACTION7chain 'C' and (resid 55 through 78 )
8X-RAY DIFFRACTION8chain 'C' and (resid 79 through 99 )

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