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- PDB-3v2y: Crystal Structure of a Lipid G protein-Coupled Receptor at 2.80A -

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Basic information

Entry
Database: PDB / ID: 3v2y
TitleCrystal Structure of a Lipid G protein-Coupled Receptor at 2.80A
ComponentsSphingosine 1-phosphate receptor 1, Lysozyme chimera (E.C.3.2.1.17)
KeywordsHYDROLASE / sphingosine / EDG receptor / lipid receptor / multiple sclerosis / autoimmunity / Structural Genomics / PSI-Biology / GPCR Network / GPCR / membrane protein / G protein coupled receptor / membrane
Function / homology
Function and homology information


cardiac muscle tissue growth involved in heart morphogenesis / sphingosine-1-phosphate receptor activity / sphingolipid binding / blood vessel maturation / Lysosphingolipid and LPA receptors / T cell migration / endothelial cell differentiation / heart trabecula morphogenesis / regulation of metabolic process / regulation of bone mineralization ...cardiac muscle tissue growth involved in heart morphogenesis / sphingosine-1-phosphate receptor activity / sphingolipid binding / blood vessel maturation / Lysosphingolipid and LPA receptors / T cell migration / endothelial cell differentiation / heart trabecula morphogenesis / regulation of metabolic process / regulation of bone mineralization / sphingosine-1-phosphate receptor signaling pathway / leukocyte chemotaxis / regulation of bone resorption / positive regulation of positive chemotaxis / lamellipodium assembly / negative regulation of stress fiber assembly / transmission of nerve impulse / regulation of cell adhesion / viral release from host cell by cytolysis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / peptidoglycan catabolic process / G protein-coupled receptor binding / G protein-coupled receptor activity / positive regulation of smooth muscle cell proliferation / brain development / adenylate cyclase-activating G protein-coupled receptor signaling pathway / neuron differentiation / chemotaxis / cell migration / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / phospholipase C-activating G protein-coupled receptor signaling pathway / actin cytoskeleton organization / angiogenesis / Interleukin-4 and Interleukin-13 signaling / cell population proliferation / host cell cytoplasm / Potential therapeutics for SARS / cell adhesion / endosome / positive regulation of cell migration / defense response to bacterium / membrane raft / G protein-coupled receptor signaling pathway / external side of plasma membrane / intracellular membrane-bounded organelle / positive regulation of transcription by RNA polymerase II / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
EDG-1 sphingosine 1-phosphate receptor / Sphingosine 1-phosphate receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme ...EDG-1 sphingosine 1-phosphate receptor / Sphingosine 1-phosphate receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Lysozyme-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-ML5 / Endolysin / Sphingosine 1-phosphate receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHanson, M.A. / Roth, C.B. / Jo, E. / Griffith, M.T. / Scott, F.L. / Reinhart, G. / Desale, H. / Clemons, B. / Cahalan, S.M. / Schuerer, S.C. ...Hanson, M.A. / Roth, C.B. / Jo, E. / Griffith, M.T. / Scott, F.L. / Reinhart, G. / Desale, H. / Clemons, B. / Cahalan, S.M. / Schuerer, S.C. / Sanna, M.G. / Han, G.W. / Kuhn, P. / Rosen, H. / Stevens, R.C. / GPCR Network (GPCR)
CitationJournal: Science / Year: 2012
Title: Crystal structure of a lipid G protein-coupled receptor.
Authors: Hanson, M.A. / Roth, C.B. / Jo, E. / Griffith, M.T. / Scott, F.L. / Reinhart, G. / Desale, H. / Clemons, B. / Cahalan, S.M. / Schuerer, S.C. / Sanna, M.G. / Han, G.W. / Kuhn, P. / Rosen, H. / Stevens, R.C.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2Jun 21, 2017Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: diffrn_radiation_wavelength / entity ...diffrn_radiation_wavelength / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3Jul 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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sphingosine 1-phosphate receptor 1, Lysozyme chimera (E.C.3.2.1.17)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5373
Polymers58,9731
Non-polymers5642
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.940, 69.700, 81.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1211-

HOH

DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Sphingosine 1-phosphate receptor 1, Lysozyme chimera (E.C.3.2.1.17) / S1P1 / Endothelial differentiation G-protein coupled receptor 1 / Sphingosine 1-phosphate receptor ...S1P1 / Endothelial differentiation G-protein coupled receptor 1 / Sphingosine 1-phosphate receptor Edg-1 / S1P receptor Edg-1 / Lysis protein / Lysozyme / Muramidase


Mass: 58973.168 Da / Num. of mol.: 1 / Mutation: C1054T, C1097A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: S1PR1, CHEDG1, EDG1 / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P21453, UniProt: P00720, lysozyme
#2: Chemical ChemComp-ML5 / {(3R)-3-amino-4-[(3-hexylphenyl)amino]-4-oxobutyl}phosphonic acid


Mass: 342.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H27N2O4P
#3: 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 / N-Acetylglucosamine


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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT THE SEQUENCE "NV" IS THE ORIGINAL SEQUENCE FROM ENDOTHELIUM, AS OPPOSED TO ...THE AUTHORS STATE THAT THE SEQUENCE "NV" IS THE ORIGINAL SEQUENCE FROM ENDOTHELIUM, AS OPPOSED TO KSL WHICH IS THE GENOMIC SEQUENCE. THE UNIPROT RECORD WAS CHANGED TO THE GENOMIC SEQUENCE "KSL" AFTER THE CLONE WAS CREATED AND THE CONSTRUCT WAS NOT CHANGED BECAUSE IT WAS PERFORMING WELL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 77

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 287 K / Method: lipidic cubic phase
Details: 0.1M Tricine, 34-36% PEG400, 80mM sodium citrate and 4% glycerol, Lipid cubic phase, temperature 287K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 23-ID-B1
SYNCHROTRONAPS 23-ID-D2
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 15297 / % possible obs: 97.2 % / Redundancy: 6 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.9 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
Microdiffactiondata assembly methodsdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TM of b2AR and T4L

Resolution: 2.8→19.52 Å / Cor.coef. Fo:Fc: 0.9055 / Cor.coef. Fo:Fc free: 0.8586 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 742 4.86 %RANDOM
Rwork0.2287 ---
obs0.2307 15275 --
Displacement parametersBiso mean: 76.61 Å2
Baniso -1Baniso -2Baniso -3
1-7.5487 Å20 Å20 Å2
2--1.2749 Å20 Å2
3----8.8236 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 0 37 11 3523
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013585HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.654893HARMONIC3
X-RAY DIFFRACTIONt_dihedral_angle_d1597SINUSOIDAL20
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes529HARMONIC5
X-RAY DIFFRACTIONt_it3585HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion2.2
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion511SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4387SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2762 125 4.72 %
Rwork0.2596 2522 -
all0.2604 2647 -
Refinement TLS params.Method: refined / Origin x: 17.1445 Å / Origin y: 18.5316 Å / Origin z: 13.5414 Å
111213212223313233
T0.2273 Å20.0573 Å2-0.0048 Å2--0.0572 Å20.0225 Å2---0.1172 Å2
L1.7528 °2-0.2526 °20.7309 °2-0 °2-0.5602 °2--0.4655 °2
S0.0421 Å °-0.2737 Å °-0.1428 Å °-0.1301 Å °-0.0121 Å °-0.0197 Å °0.0116 Å °-0.0999 Å °-0.03 Å °
Refinement TLS groupSelection details: chain A

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