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- PDB-4dlq: Crystal structure of the GAIN and HormR domains of CIRL 1/Latroph... -

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Basic information

Entry
Database: PDB / ID: 4dlq
TitleCrystal structure of the GAIN and HormR domains of CIRL 1/Latrophilin 1 (CL1)
Components(Latrophilin-1) x 2
KeywordsSIGNALING PROTEIN / GAIN domain / includes the GPS motif / hormone binding domain / autoproteolysis / a-latrotoxin / extracellular domain
Function / homology
Function and homology information


latrotoxin receptor activity / positive regulation of synapse maturation / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / : / toxic substance binding / cell adhesion molecule binding / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / presynaptic membrane ...latrotoxin receptor activity / positive regulation of synapse maturation / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / : / toxic substance binding / cell adhesion molecule binding / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / presynaptic membrane / growth cone / carbohydrate binding / cell surface receptor signaling pathway / neuron projection / axon / glutamatergic synapse / synapse / plasma membrane
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #610 / Chondroitinase Ac; Chain A, domain 3 - #50 / Latrophilin-1 / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / GPCR, family 2, extracellular hormone receptor domain / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #610 / Chondroitinase Ac; Chain A, domain 3 - #50 / Latrophilin-1 / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / GPCR, family 2, extracellular hormone receptor domain / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / Hormone receptor fold / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / Chondroitinase Ac; Chain A, domain 3 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / 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 / 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. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Few Secondary Structures / Irregular / Alpha Horseshoe / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Adhesion G protein-coupled receptor L1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsArac, D. / Boucard, A.A. / Bolliger, M.F. / Nguyen, J. / Soltis, M. / Sudhof, T.C. / Brunger, A.T.
CitationJournal: Embo J. / Year: 2012
Title: A novel evolutionarily conserved domain of cell-adhesion GPCRs mediates autoproteolysis.
Authors: Arac, D. / Boucard, A.A. / Bolliger, M.F. / Nguyen, J. / Soltis, S.M. / Sudhof, T.C. / Brunger, A.T.
History
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
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: Latrophilin-1
B: Latrophilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,46717
Polymers44,2052
Non-polymers2,26215
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-91 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.000, 124.000, 77.305
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-910-

SO4

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Latrophilin-1 / Calcium-independent alpha-latrotoxin receptor 1 / CIRL-1


Mass: 41947.492 Da / Num. of mol.: 1
Fragment: GAIN and HormR domains of CL1, UNP residues 460-837
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Lphn1, Cirl, Cirl1, Cl1 / Production host: Trichoplusia Ni (cabbage looper) / References: UniProt: O88917
#2: Protein/peptide Latrophilin-1 / Calcium-independent alpha-latrotoxin receptor 1 / CIRL-1


Mass: 2257.556 Da / Num. of mol.: 1 / Fragment: UNP residues 838-850
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Lphn1, Cirl, Cirl1, Cl1 / Production host: Trichoplusia Ni (cabbage looper) / References: UniProt: O88917

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Sugars , 2 types, 5 molecules

#3: 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
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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 , 3 types, 285 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.26M (NH4)2SO4, 0.1M sodium acetate pH 4.5, 0.2M NaCl,, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1651
2651
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111
SYNCHROTRONSSRL BL9-222
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDJul 7, 2009
MARMOSAIC 325 mm CCD2CCDJul 7, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degsSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
221
ReflectionResolution: 1.85→35.9 Å / Num. all: 58629 / Num. obs: 58546 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.85-1.881,295.2
1.88-1.921,298.8
1.92-1.951,299.8
1.95-1.991,2100
1.99-2.041,2100
2.04-2.081,2100
2.08-2.141,2100
2.14-2.191,2100
2.19-2.261,2100
2.26-2.331,2100
5.02-501,299.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→35.9 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 16.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 2936 5.01 %random
Rwork0.1635 ---
obs0.1646 58546 99.87 %-
all-58629 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.597 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8244 Å20 Å2-0 Å2
2--1.8244 Å20 Å2
3----3.6488 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 136 275 3268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083086
X-RAY DIFFRACTIONf_angle_d1.0924195
X-RAY DIFFRACTIONf_dihedral_angle_d17.7261143
X-RAY DIFFRACTIONf_chiral_restr0.082486
X-RAY DIFFRACTIONf_plane_restr0.005528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.88040.28271280.24732550X-RAY DIFFRACTION98
1.8804-1.91280.26131230.22582625X-RAY DIFFRACTION100
1.9128-1.94760.26391350.19882653X-RAY DIFFRACTION100
1.9476-1.98510.19071430.18232614X-RAY DIFFRACTION100
1.9851-2.02560.19291410.17642626X-RAY DIFFRACTION100
2.0256-2.06960.20861450.15822627X-RAY DIFFRACTION100
2.0696-2.11770.1771560.15172609X-RAY DIFFRACTION100
2.1177-2.17070.17451400.15082633X-RAY DIFFRACTION100
2.1707-2.22940.17091330.13972632X-RAY DIFFRACTION100
2.2294-2.2950.18691250.14522654X-RAY DIFFRACTION100
2.295-2.3690.17921310.15032644X-RAY DIFFRACTION100
2.369-2.45370.18031590.14842620X-RAY DIFFRACTION100
2.4537-2.55190.17041190.14872669X-RAY DIFFRACTION100
2.5519-2.6680.2121320.15932661X-RAY DIFFRACTION100
2.668-2.80860.16571500.15962630X-RAY DIFFRACTION100
2.8086-2.98450.19211640.16152651X-RAY DIFFRACTION100
2.9845-3.21480.19421490.16432648X-RAY DIFFRACTION100
3.2148-3.53810.16591560.14452643X-RAY DIFFRACTION100
3.5381-4.04950.14361430.13452700X-RAY DIFFRACTION100
4.0495-5.09960.13661330.13742708X-RAY DIFFRACTION100
5.0996-35.94310.22421310.18842813X-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)
10.74060.4737-0.20120.96820.67540.951-0.04950.0412-0.05880.03-0.05450.0696-0.1234-0.107500.15530.04240.00030.1969-0.02160.163853.358240.204810.6921
20.4494-0.3195-0.47840.49610.03420.6515-0.1373-0.08240.2552-0.0218-0.08220.1371-0.1123-0.728400.19890.0631-0.03160.4722-0.06630.324634.618134.177-9.6373
30.3781-0.2789-0.26560.5995-0.01831.0451-0.20150.05280.2557-0.093-0.03170.3472-0.0445-0.420200.1481-0.04040.02350.332-0.03740.250633.717323.8585-18.4086
40.7368-0.3695-0.04490.2722-0.23690.6890.0484-0.26190.00620.1834-0.0880.16240.143-0.3209-0.00010.218-0.02410.03170.2570.01350.232144.601923.2365-8.9871
50.1611-0.41040.29910.734-0.80490.92230.11510.1209-0.011-0.2885-0.0402-0.0190.2997-0.0309-00.2722-0.0632-0.03190.1694-0.01210.162247.062514.7042-28.3377
60.5712-0.25540.19240.18450.06950.40070.0714-0.1394-0.07430.13710.04460.07180.3677-0.1033-00.3008-0.0595-0.02090.17710.03050.214150.368813.567-15.6866
70.0460.08930.30.53230.24870.35780.0241-0.05640.0820.10170.0130.09590.22110.0811-00.2357-0.00030.01120.17680.00130.178157.941914.4513-11.4585
80.5830.24110.58750.49340.23411.01110.00720.0342-0.11380.04090.0801-0.07520.21560.126800.13350.0170.00140.076-0.00270.105862.646915.7517-12.2399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 474:532 )A474 - 532
2X-RAY DIFFRACTION2( CHAIN A AND RESID 533:577 )A533 - 577
3X-RAY DIFFRACTION3( CHAIN A AND RESID 578:633 )A578 - 633
4X-RAY DIFFRACTION4( CHAIN A AND RESID 634:665 )A634 - 665
5X-RAY DIFFRACTION5( CHAIN A AND RESID 666:713 )A666 - 713
6X-RAY DIFFRACTION6( CHAIN A AND RESID 714:745 )A714 - 745
7X-RAY DIFFRACTION7( CHAIN A AND RESID 746:782 )A746 - 782
8X-RAY DIFFRACTION8( CHAIN A AND RESID 783:837 ) OR ( CHAIN B AND RESID 838:852 )A783 - 837
9X-RAY DIFFRACTION8( CHAIN A AND RESID 783:837 ) OR ( CHAIN B AND RESID 838:852 )B838 - 852

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