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- PDB-4m4z: SH3 and SH2 domains of human Src-like adaptor protein 2 (SLAP2) -

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Basic information

Entry
Database: PDB / ID: 4m4z
TitleSH3 and SH2 domains of human Src-like adaptor protein 2 (SLAP2)
ComponentsSrc-like-adapter 2
KeywordsSIGNALING PROTEIN / SH3 and SH2 domains / Adaptor
Function / homology
Function and homology information


antigen receptor-mediated signaling pathway / negative regulation of calcium-mediated signaling / B cell mediated immunity / : / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex / negative regulation of T cell receptor signaling pathway / phosphatidylinositol phosphate biosynthetic process / regulation of immune response / signaling adaptor activity ...antigen receptor-mediated signaling pathway / negative regulation of calcium-mediated signaling / B cell mediated immunity / : / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex / negative regulation of T cell receptor signaling pathway / phosphatidylinositol phosphate biosynthetic process / regulation of immune response / signaling adaptor activity / T cell activation / late endosome / endosome membrane / intracellular membrane-bounded organelle / Golgi apparatus / negative regulation of transcription by RNA polymerase II / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Src-like-adapter 2 / SLAP, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. ...Src-like-adapter 2 / SLAP, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsWybenga-Groot, L.E. / McGlade, C.J.
CitationJournal: Cell Signal / Year: 2013
Title: Crystal structure of Src-like adaptor protein 2 reveals close association of SH3 and SH2 domains through beta-sheet formation.
Authors: Wybenga-Groot, L.E. / McGlade, C.J.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Src-like-adapter 2


Theoretical massNumber of molelcules
Total (without water)18,7861
Polymers18,7861
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.460, 42.430, 46.100
Angle α, β, γ (deg.)90.000, 94.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Src-like-adapter 2 / Modulator of antigen receptor signaling / MARS / Src-like adapter protein 2 / SLAP-2


Mass: 18786.291 Da / Num. of mol.: 1 / Fragment: UNP residues 29-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C20orf156, SLA2, SLAP2 / Plasmid: pETM-30-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9H6Q3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Lithium chloride, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 11, 2013
RadiationMonochromator: VARIMAX VHF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→31.17 Å / Num. all: 8539 / Num. obs: 8539 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.5
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 4.8 / Num. unique all: 687 / % possible all: 95.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å28.44 Å
Translation3 Å28.44 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA0.1.29data scaling
PHASER2.5.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCK

1lck


Resolution: 2.1→28.445 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.24 / σ(F): 1.35 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.225 428 5.02 %Random
Rwork0.1817 ---
obs0.1839 8528 97.03 %-
all-8528 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.25 Å2 / Biso mean: 41.9821 Å2 / Biso min: 14.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 0 64 1247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041232
X-RAY DIFFRACTIONf_angle_d0.7571683
X-RAY DIFFRACTIONf_chiral_restr0.049188
X-RAY DIFFRACTIONf_plane_restr0.004212
X-RAY DIFFRACTIONf_dihedral_angle_d12.23434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.40380.28551400.21092641278195
2.4038-3.0280.31211460.2142679282597
3.028-28.4450.17171420.15982780292298
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)
12.33063.6678-1.51615.9099-1.71054.81450.01220.584-0.0916-0.8378-0.0449-0.7237-0.63880.68290.18310.3155-0.04770.04750.30050.04350.28011.6-7.0847-15.8333
21.66430.25731.30680.30360.08051.07880.0190.66230.1899-0.2140.27210.2551-0.184-0.28320.00820.95830.2388-0.13860.59080.13040.252-6.4274-3.061-25.5381
33.36570.7345-2.70315.2298-0.12192.21460.28510.32430.56080.2118-0.35160.108-0.9344-0.0381-0.26670.7888-0.0922-0.03320.3610.17220.2071-0.8272-3.7666-22.9225
44.90672.6846-3.57513.259-3.11013.3543-0.31440.2788-0.2175-1.10260.0375-0.3316-0.3097-0.03780.20160.5348-0.08110.05240.4650.02020.2086-2.471-8.5292-22.3053
56.8813-5.0886-3.67063.77052.79875.63450.5040.96560.721-0.3027-0.3861-0.1887-0.2321-0.4975-0.1830.26050.03930.06090.33130.12440.3148-13.7142-6.7603-11.6705
68.26011.2303-2.7320.789-2.20236.41140.04040.0460.2244-0.08490.0469-0.68260.13330.2659-0.15920.15090.0208-0.00680.1240.03980.2792-5.1607-11.825-3.3513
74.5252-0.7262-0.70192.6362-1.11751.24860.21080.3165-0.5513-0.1557-0.10850.28660.252-0.0086-0.10150.17390-0.04030.1682-0.04190.2432-17.0181-15.3722-3.6
81.39032.1370.97213.71962.03211.3517-0.4112-0.5805-1.1787-0.0422-0.19320.16850.81950.00030.08610.2355-0.00730.07660.25670.09090.4641-30.0388-9.7094-1.9861
98.2716-2.6583-0.37741.77281.34024.6014-0.241-0.24940.4798-0.00870.1461-0.2707-0.0165-0.08150.09530.16040.01630.03310.1295-0.01620.2631-19.031-6.02512.2516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 58 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 65 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 78 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 89 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 100 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 117 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 118 through 161 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 162 through 168 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 169 through 192 )A0

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