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- PDB-1oeb: Mona/Gads SH3C domain -

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Basic information

Entry
Database: PDB / ID: 1oeb
TitleMona/Gads SH3C domain
Components
  • GRB2-RELATED ADAPTOR PROTEIN 2
  • LYMPHOCYTE CYTOSOLIC PROTEIN 2
KeywordsPROTEIN BINDING / SH3 DOMAIN-COMPLEX / SH3 / SLP-76 / DIMER / MONA / GADS / SIGNAL TRANDUCTION
Function / homology
Function and homology information


TCR signalosome / FLT3 Signaling / Co-stimulation by CD28 / GPVI-mediated activation cascade / FCERI mediated MAPK activation / Signaling by SCF-KIT / Generation of second messenger molecules / mast cell activation / FCERI mediated Ca+2 mobilization / DAP12 signaling ...TCR signalosome / FLT3 Signaling / Co-stimulation by CD28 / GPVI-mediated activation cascade / FCERI mediated MAPK activation / Signaling by SCF-KIT / Generation of second messenger molecules / mast cell activation / FCERI mediated Ca+2 mobilization / DAP12 signaling / plasma membrane raft / cell-cell junction / T cell receptor signaling pathway / endosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
GRAP2, C-terminal SH3 domain / : / Grb2-like / SAM domain (Sterile alpha motif) / SH3 Domains / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH3 domain / SH2 domain ...GRAP2, C-terminal SH3 domain / : / Grb2-like / SAM domain (Sterile alpha motif) / SH3 Domains / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
: / GRB2-related adaptor protein 2 / Lymphocyte cytosolic protein 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å
AuthorsHarkiolaki, M. / Lewitzky, M. / Gilbert, R.J.C. / Jones, E.Y. / Bourette, R.P. / Mouchiroud, G. / Sondermann, H. / Moarefi, I. / Feller, S.M.
CitationJournal: Embo J. / Year: 2003
Title: Structural Basis for SH3 Domain-Mediated High-Affinity Binding between Mona/Gads and Slp-76
Authors: Harkiolaki, M. / Lewitzky, M. / Gilbert, R.J.C. / Jones, E.Y. / Bourette, R.P. / Mouchiroud, G. / Sondermann, H. / Moarefi, I. / Feller, S.M.
History
DepositionMar 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GRB2-RELATED ADAPTOR PROTEIN 2
B: GRB2-RELATED ADAPTOR PROTEIN 2
C: LYMPHOCYTE CYTOSOLIC PROTEIN 2
D: LYMPHOCYTE CYTOSOLIC PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0525
Polymers16,9394
Non-polymers1121
Water4,288238
1
A: GRB2-RELATED ADAPTOR PROTEIN 2
D: LYMPHOCYTE CYTOSOLIC PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5823
Polymers8,4702
Non-polymers1121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GRB2-RELATED ADAPTOR PROTEIN 2
C: LYMPHOCYTE CYTOSOLIC PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)8,4702
Polymers8,4702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)28.691, 72.072, 34.168
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TRPTRPPROPRO2AA3 - 557 - 59
21TRPTRPPROPRO2BB3 - 557 - 59
12ALAALALEULEU4CC2 - 132 - 13
22ALAALALEULEU4DD2 - 132 - 13

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.99919, 0.03727, -0.01508), (-0.03854, -0.99437, 0.09499), (-0.01146, 0.09549, 0.99536)4.09705, 6.12949, -0.31041
2given(-0.99876, 0.04884, 0.00968), (0.04954, -0.99419, 0.09556), (0.00496, 0.09592, 0.99538)4.09731, 5.6547, -0.52231

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Components

#1: Protein GRB2-RELATED ADAPTOR PROTEIN 2 / GADS PROTEIN / GROWTH FACTOR RECEPTOR PROTEIN / GRBLG / GRF40 ADAPTOR PROTEIN / GRF-40 / GRB-2-LIKE ...GADS PROTEIN / GROWTH FACTOR RECEPTOR PROTEIN / GRBLG / GRF40 ADAPTOR PROTEIN / GRF-40 / GRB-2-LIKE PROTEIN / GRB2L / GRBX / P38 / HEMATOPOIETIC CELL-ASSOCIATED ADAPTOR PROTEIN GRPL / ADAPTER PROTEIN GRID / SH3-SH2-SH3 ADAPTOR MONA


Mass: 7088.970 Da / Num. of mol.: 2 / Fragment: SH3C DOMAIN, RESIDUES 265-322
Source method: isolated from a genetically manipulated source
Details: THROMBIN CLEAVAGE OVERHANG BETWEEN A-4 AND A-1 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O89100
#2: Protein/peptide LYMPHOCYTE CYTOSOLIC PROTEIN 2 / SH2 DOMAIN-CONTAINING LEUCOCYTE PROTEIN OF 76 KDA / SLP-76 TYROSINE PHOSPHOPROTEIN / SLP76


Mass: 1380.589 Da / Num. of mol.: 2 / Fragment: PROTEIN INTERACTION PEPTIDE, RESIDUES 231-243 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q60787
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGADS/MONA:INTERACTS WITH SLP-76 TO REGULATE NF-AT ACTIVATION. SLP-76:INVOLVED IN T CELL ANTIGEN ...GADS/MONA:INTERACTS WITH SLP-76 TO REGULATE NF-AT ACTIVATION. SLP-76:INVOLVED IN T CELL ANTIGEN RECEPTOR MEDIATED SIGNALING
Sequence detailsSELENOMETHIONYL MONA/GADS SH3C WAS PRODUCED IN BL21(DE3) CELLS BY INHIBITION OF ENDOGENOUS ...SELENOMETHIONYL MONA/GADS SH3C WAS PRODUCED IN BL21(DE3) CELLS BY INHIBITION OF ENDOGENOUS METHIONINE PRODUCTION AND SUPPLEMENTATION WITH SELENOMETHIONINE THROUGH THE MEDIUM.

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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: 1.9 Å3/Da / Density % sol: 36.3 %
Description: MAD DATA COLLECTED AT SELENIUM PEAK, INFLECTION AND HIGH ENERGY REMOTE WAVELENGTHS. DATA STATISTICS REFLECT THE PEAK WAVELENGTH.
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLISED FROM: 20% PEG4000, 5 MM CDCL2,50 MM NA CACODYLATE PH 6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 %PEG40001reservoir
25 mM1reservoirCdCl2
350 mMsodium cacodylate1reservoirpH6.5
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9786
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2002 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.69→36 Å / Num. obs: 15317 / % possible obs: 98 % / Observed criterion σ(I): 4 / Redundancy: 6.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 28.2
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 4 / % possible all: 81.4
Reflection
*PLUS
Lowest resolution: 36 Å / % possible obs: 98.2 % / Num. measured all: 99470
Reflection shell
*PLUS
% possible obs: 81.4 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.76→19.69 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.097 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.235 652 4.9 %RANDOM
Rwork0.171 ---
obs0.174 12567 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.76→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1098 0 1 238 1337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211130
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9551537
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0675133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1150.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02879
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.2491
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.20.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9381.5690
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.721104
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8653440
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3684.5433
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A212tight positional0.090.05
1A218medium positional0.390.5
2C89medium positional0.250.5
1A212tight thermal0.440.5
1A218medium thermal1.282
2C89medium thermal1.32
LS refinement shellResolution: 1.76→1.8 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 39
Rwork0.253 895
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 36.04 Å / Num. reflection obs: 13807 / % reflection Rfree: 5 % / Rfactor Rfree: 0.2194 / Rfactor Rwork: 0.1786
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_d0.0120.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3751.955
X-RAY DIFFRACTIONr_chiral_restr4.8275

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