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- PDB-5xws: Crystal structure of SALM5 LRR-Ig -

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Basic information

Entry
Database: PDB / ID: 5xws
TitleCrystal structure of SALM5 LRR-Ig
ComponentsLeucine-rich repeat and fibronectin type-III domain-containing protein 5
KeywordsCELL ADHESION / synaptic orgnizers
Function / homology
Function and homology information


negative regulation of macrophage activation / synaptic membrane adhesion / regulation of presynapse assembly / GABA-ergic synapse / postsynaptic density membrane / negative regulation of inflammatory response / glutamatergic synapse / cell surface
Similarity search - Function
BspA type Leucine rich repeat region (6 copies) / Immunoglobulin domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set domain / Leucine-rich repeat profile. / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...BspA type Leucine rich repeat region (6 copies) / Immunoglobulin domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set domain / Leucine-rich repeat profile. / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Leucine-rich repeat domain superfamily / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Leucine-rich repeat and fibronectin type-III domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.084 Å
AuthorsGoto-Ito, S. / Yamagata, A. / Sato, Y. / Fukai, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
JST CREST Japan
MEXT/JSPS22121003 Japan
MEXT/JSPS16H04749 Japan
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation.
Authors: Goto-Ito, S. / Yamagata, A. / Sato, Y. / Uemura, T. / Shiroshima, T. / Maeda, A. / Imai, A. / Mori, H. / Yoshida, T. / Fukai, S.
History
DepositionJun 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Leucine-rich repeat and fibronectin type-III domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8082
Polymers41,3831
Non-polymers4241
Water0
1
A: Leucine-rich repeat and fibronectin type-III domain-containing protein 5
hetero molecules

A: Leucine-rich repeat and fibronectin type-III domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6164
Polymers82,7672
Non-polymers8492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/21
Unit cell
Length a, b, c (Å)154.888, 154.888, 91.262
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Leucine-rich repeat and fibronectin type-III domain-containing protein 5


Mass: 41383.496 Da / Num. of mol.: 1 / Fragment: UNP residues 18-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRFN5, C14orf146, SALM5 / Production host: Homo sapiens (human) / References: UniProt: Q96NI6
#2: 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

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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: 3.82 Å3/Da / Density % sol: 67.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 3350, 0.2M ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 12254 / % possible obs: 100 % / Redundancy: 16.9 % / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.084→44.712 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 35.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3084 610 4.98 %
Rwork0.2681 --
obs0.2701 12253 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.084→44.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 28 0 2181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022233
X-RAY DIFFRACTIONf_angle_d0.7393035
X-RAY DIFFRACTIONf_dihedral_angle_d9.966829
X-RAY DIFFRACTIONf_chiral_restr0.046365
X-RAY DIFFRACTIONf_plane_restr0.004386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.084-3.39420.3831500.33262749X-RAY DIFFRACTION96
3.3942-3.88510.29251320.27262896X-RAY DIFFRACTION100
3.8851-4.89390.23741550.23312920X-RAY DIFFRACTION100
4.8939-44.7170.34711730.27413078X-RAY DIFFRACTION100

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