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- PDB-6v55: Full extracellular region of zebrafish Gpr126/Adgrg6 -

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Basic information

Entry
Database: PDB / ID: 6v55
TitleFull extracellular region of zebrafish Gpr126/Adgrg6
Components(Adhesion G-protein coupled receptor G6) x 2
KeywordsCELL ADHESION / adhesion G-protein coupled receptor / myelination / calcium-binding
Function / homology
Function and homology information


myelination of posterior lateral line nerve axons / EGR2 and SOX10-mediated initiation of Schwann cell myelination / semicircular canal fusion / regulation of sprouting angiogenesis / Schwann cell differentiation / peripheral nervous system myelin formation / ear development / myelination in peripheral nervous system / heart trabecula formation / extracellular matrix binding ...myelination of posterior lateral line nerve axons / EGR2 and SOX10-mediated initiation of Schwann cell myelination / semicircular canal fusion / regulation of sprouting angiogenesis / Schwann cell differentiation / peripheral nervous system myelin formation / ear development / myelination in peripheral nervous system / heart trabecula formation / extracellular matrix binding / laminin binding / collagen binding / myelination / mitochondrion organization / cAMP-mediated signaling / ossification / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / heart development / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / plasma membrane
Similarity search - Function
Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / CUB domain ...Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Adhesion G-protein coupled receptor G6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.38 Å
AuthorsLeon, K. / Arac, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120322 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for adhesion G protein-coupled receptor Gpr126 function.
Authors: Leon, K. / Cunningham, R.L. / Riback, J.A. / Feldman, E. / Li, J. / Sosnick, T.R. / Zhao, M. / Monk, K.R. / Arac, D.
History
DepositionDec 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
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: Adhesion G-protein coupled receptor G6
Q: Adhesion G-protein coupled receptor G6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,25914
Polymers87,7852
Non-polymers2,47312
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint10 kcal/mol
Surface area36180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.960, 59.448, 168.385
Angle α, β, γ (deg.)90.000, 107.821, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1141-

HOH

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Components

#1: Protein Adhesion G-protein coupled receptor G6 / G-protein coupled receptor 126


Mass: 86436.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: adgrg6, gpr126 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C6KFA3
#2: Protein/peptide Adhesion G-protein coupled receptor G6 / G-protein coupled receptor 126


Mass: 1348.571 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: adgrg6, gpr126 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C6KFA3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4 Å3/Da / Density % sol: 69.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 50mM potassium dihydrogen phosphate, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033, 0.979
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
20.9791
ReflectionResolution: 2.38→47.9 Å / Num. obs: 43044 / % possible obs: 77.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 24.25 Å2 / CC1/2: 0.557 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15
Reflection shellResolution: 2.38→2.46 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 686 / CC1/2: 0.557 / % possible all: 25.4

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.38→47.9 Å / SU ML: 0.2773 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.2717
RfactorNum. reflection% reflection
Rfree0.2717 1752 5.09 %
Rwork0.2121 --
obs0.2152 34405 62.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.29 Å2
Refinement stepCycle: LAST / Resolution: 2.38→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5762 0 155 197 6114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016027
X-RAY DIFFRACTIONf_angle_d1.20598218
X-RAY DIFFRACTIONf_chiral_restr0.06831008
X-RAY DIFFRACTIONf_plane_restr0.00791039
X-RAY DIFFRACTIONf_dihedral_angle_d7.4868857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.440.4169160.2841268X-RAY DIFFRACTION6.79
2.44-2.520.316340.3113583X-RAY DIFFRACTION14.92
2.52-2.60.377580.2972909X-RAY DIFFRACTION22.93
2.6-2.690.3507700.29571326X-RAY DIFFRACTION33.01
2.69-2.80.3339840.29271737X-RAY DIFFRACTION42.94
2.8-2.920.35921030.29742188X-RAY DIFFRACTION54.66
2.92-3.080.33411550.27272660X-RAY DIFFRACTION66.58
3.08-3.270.34421690.24723054X-RAY DIFFRACTION75.68
3.27-3.520.30691830.22453583X-RAY DIFFRACTION88.82
3.52-3.880.28862330.19314013X-RAY DIFFRACTION99.86
3.88-4.440.23722070.16374057X-RAY DIFFRACTION99.98
4.44-5.590.19362020.16474114X-RAY DIFFRACTION99.93
5.59-47.90.23282380.21374161X-RAY DIFFRACTION99.75
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)
10.1431916041050.05637313204280.02319213986090.0255158918347-0.02715120893260.122561385376-0.1804389721190.332002129145-0.0947911735492-0.01862589801210.107862842341-0.09365571160740.2056252917930.117304502679-0.09874593594680.2473772629410.2002686648030.06351750561530.601064183646-0.03428290263580.03755181381017.80978528545-38.5188491119-68.292331473
20.793180668983-0.414554315059-0.2446012899230.2532817277820.09473663678150.1940260665760.01448711326850.0772720619170.09104350450080.0164407113703-0.0101077962177-0.02683728707370.03671162810080.09729165348840.01969738484780.1593604504180.265516629287-0.02774093020510.326776992730.1062440079260.1169105224847.32055189452-19.987571584-34.3247165962
30.839322011696-0.2380480632270.0299745440261.19694053038-0.3362429805621.543786582250.0580976066186-0.0419488534554-0.09732461072980.182978760324-0.03200725433480.2800720451940.302135512139-0.140615294492-0.07111597025260.3436380182350.07495268769060.1011103751550.08602949702070.02734700571060.0624572414081-36.8425069563-13.1115200996-14.8998947702
47.48590764726-2.14753295582-0.6414968635676.02306925747-3.933172470253.18997984029-0.105524911861-0.351613220067-0.5419861565880.888193500580.3250248160050.2944568084020.241542740019-0.296793196919-0.213673456030.493360237693-0.08310197656940.01110814809390.1987041310120.01740091471360.188108241471-37.1412617056-19.1957837624-9.23041629617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 398 )
2X-RAY DIFFRACTION2chain 'A' and (resid 399 through 554 )
3X-RAY DIFFRACTION3chain 'A' and (resid 555 through 768 )
4X-RAY DIFFRACTION4chain 'Q' and (resid 769 through 778 )

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