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- PDB-6tl8: Structural basis of SALM3 dimerization and adhesion complex forma... -

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Basic information

Entry
Database: PDB / ID: 6tl8
TitleStructural basis of SALM3 dimerization and adhesion complex formation with the presynaptic receptor protein tyrosine phosphatases
ComponentsMyeloid cell surface antigen CD33,Leucine-rich repeat and fibronectin type-III domain-containing protein 4
KeywordsCELL ADHESION / LEUCINE RICH REPEAT / SYNAPSE / SALM3
Function / homology
Function and homology information


immune response-inhibiting signal transduction / positive regulation of protein tyrosine phosphatase activity / Synaptic adhesion-like molecules / negative regulation of monocyte activation / sialic acid binding / regulation of postsynaptic density assembly / synaptic membrane adhesion / negative regulation of interleukin-8 production / negative regulation of interleukin-1 beta production / tertiary granule membrane ...immune response-inhibiting signal transduction / positive regulation of protein tyrosine phosphatase activity / Synaptic adhesion-like molecules / negative regulation of monocyte activation / sialic acid binding / regulation of postsynaptic density assembly / synaptic membrane adhesion / negative regulation of interleukin-8 production / negative regulation of interleukin-1 beta production / tertiary granule membrane / negative regulation of calcium ion transport / negative regulation of tumor necrosis factor production / regulation of presynapse assembly / GABA-ergic synapse / specific granule membrane / positive regulation of protein secretion / postsynaptic density membrane / cell-cell adhesion / peroxisome / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell signaling / signaling receptor activity / carbohydrate binding / protein phosphatase binding / cell adhesion / negative regulation of cell population proliferation / external side of plasma membrane / glutamatergic synapse / Neutrophil degranulation / Golgi apparatus / cell surface / signal transduction / nucleoplasm / plasma membrane
Similarity search - Function
Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Immunoglobulin / Immunoglobulin domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain ...Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Immunoglobulin / Immunoglobulin domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine-rich repeat / Fibronectin type III domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Leucine-rich repeat domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Myeloid cell surface antigen CD33 / Leucine-rich repeat and fibronectin type-III domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKarki, S. / Shkumatov, A.V. / Bae, S. / Ko, J. / Kajander, T.
Funding support Finland, 1items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation Finland
CitationJournal: Sci Rep / Year: 2020
Title: Structural basis of SALM3 dimerization and synaptic adhesion complex formation with PTP sigma.
Authors: Karki, S. / Shkumatov, A.V. / Bae, S. / Kim, H. / Ko, J. / Kajander, T.
History
DepositionDec 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloid cell surface antigen CD33,Leucine-rich repeat and fibronectin type-III domain-containing protein 4
B: Myeloid cell surface antigen CD33,Leucine-rich repeat and fibronectin type-III domain-containing protein 4
C: Myeloid cell surface antigen CD33,Leucine-rich repeat and fibronectin type-III domain-containing protein 4
D: Myeloid cell surface antigen CD33,Leucine-rich repeat and fibronectin type-III domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9526
Polymers130,5104
Non-polymers4422
Water32418
1
A: Myeloid cell surface antigen CD33,Leucine-rich repeat and fibronectin type-III domain-containing protein 4
D: Myeloid cell surface antigen CD33,Leucine-rich repeat and fibronectin type-III domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4763
Polymers65,2552
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-5 kcal/mol
Surface area21890 Å2
MethodPISA
2
B: Myeloid cell surface antigen CD33,Leucine-rich repeat and fibronectin type-III domain-containing protein 4
C: Myeloid cell surface antigen CD33,Leucine-rich repeat and fibronectin type-III domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4763
Polymers65,2552
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-2 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.450, 132.160, 134.180
Angle α, β, γ (deg.)90.000, 90.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Myeloid cell surface antigen CD33,Leucine-rich repeat and fibronectin type-III domain-containing protein 4 / Sialic acid-binding Ig-like lectin 3 / Siglec-3 / gp67


Mass: 32627.439 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: - "MPLLLLLPLLWAGALA" aminoacid residues in n-terminal are from CD33 signal peptide - "MDK" residues in n-terminal are the residues from Drosophila pRMHA3 expression vector - "GTRGSL " ...Details: - "MPLLLLLPLLWAGALA" aminoacid residues in n-terminal are from CD33 signal peptide - "MDK" residues in n-terminal are the residues from Drosophila pRMHA3 expression vector - "GTRGSL " residues in c-terminal are from Drosophila pRMHA3 expression vector - "EVLFQ" residues in c-terminal are residues from Prescission protease,- "MPLLLLLPLLWAGALA" aminoacid residues in n-terminal are from CD33 signal peptide - "MDK" residues in n-terminal are the residues from Drosophila pRMHA3 expression vector - "GTRGSL " residues in c-terminal are from Drosophila pRMHA3 expression vector - "EVLFQ" residues in c-terminal are residues from Prescission protease
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse)
Gene: CD33, SIGLEC3, Lrfn4, Salm3 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P20138, UniProt: Q80XU8
#2: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.17 M ammonium sulfate pH 7.5, 25% w/v PEG 4000, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 26991 / % possible obs: 99.17 % / Redundancy: 5.9 % / Biso Wilson estimate: 80.02 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.17 / Net I/av σ(I): 8.9 / Net I/σ(I): 9
Reflection shellResolution: 2.79→2.87 Å / Rmerge(I) obs: 1.19 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1886 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 6F2O

6f2o


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.872 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.398
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1347 5.01 %RANDOM
Rwork0.2619 ---
obs0.2631 26902 99.6 %-
Displacement parametersBiso max: 134.16 Å2 / Biso mean: 88.27 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--3.2735 Å20 Å20.0099 Å2
2---2.8054 Å20 Å2
3---6.0789 Å2
Refine analyzeLuzzati coordinate error obs: 0.67 Å
Refinement stepCycle: final / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7258 0 28 18 7304
Biso mean--109.12 22.01 -
Num. residues----1010
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2324SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1283HARMONIC5
X-RAY DIFFRACTIONt_it7466HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1012SEMIHARMONIC5
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_contact4622SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7466HARMONIC20.006
X-RAY DIFFRACTIONt_angle_deg10254HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion2.06
X-RAY DIFFRACTIONt_other_torsion19.38
LS refinement shellResolution: 2.8→3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.322 27 5.01 %
Rwork0.2918 512 -
all0.2932 539 -
obs--91.92 %
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)
11.9565-0.6236-0.32156.1875-2.63363.07160.0361-0.07620.30130.0926-0.0512-0.3754-0.09160.31770.0151-0.8629-0.0561-0.01081.0193-0.0786-0.8348-29.026315.30926.5309
21.6072-0.19690.05233.1196-0.81491.1769-0.07790.121-0.29070.14610.0285-0.33030.10220.23430.0494-0.79320.04430.05481.22680.0054-0.8163-29.1982-1.57675.3762
31.9348-0.1756-0.11843.2802-0.85983.0556-0.1124-0.26580.3240.50640.20010.2097-0.7037-0.4491-0.0877-0.6483-0.0059-0.01120.9677-0.0586-0.7477-42.819814.835893.8438
41.4958-0.29520.261.6710.60511.11720.04590.2966-0.2444-0.557-0.01340.11710.5519-0.2617-0.0325-0.55980.01180.02131.1118-0.0211-0.7664-42.6784-0.69018.1282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A16 - 278
2X-RAY DIFFRACTION2{ B|* }B14 - 278
3X-RAY DIFFRACTION3{ C|* }C16 - 279
4X-RAY DIFFRACTION4{ D|* }D16 - 284

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