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- PDB-5abs: CRYSTAL STRUCTURE OF THE C-TERMINAL COILED-COIL DOMAIN OF CIN85 I... -

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Basic information

Entry
Database: PDB / ID: 5abs
TitleCRYSTAL STRUCTURE OF THE C-TERMINAL COILED-COIL DOMAIN OF CIN85 IN SPACE GROUP P321
ComponentsSH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1
KeywordsSIGNALING PROTEIN / CBL-INTERACTING PROTEIN OF 85 KDA / ADAPTER PROTEIN / COILED-COIL DOMAIN / B-CELL ANTIGEN RECEPTOR SIGNALING
Function / homology
Function and homology information


Reelin signalling pathway / positive regulation of B cell activation / endocytic vesicle / cytoskeleton organization / InlB-mediated entry of Listeria monocytogenes into host cell / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / EGFR downregulation / cytoplasmic vesicle membrane / Negative regulation of MET activity ...Reelin signalling pathway / positive regulation of B cell activation / endocytic vesicle / cytoskeleton organization / InlB-mediated entry of Listeria monocytogenes into host cell / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / EGFR downregulation / cytoplasmic vesicle membrane / Negative regulation of MET activity / SH3 domain binding / endocytosis / cell-cell junction / cell migration / Cargo recognition for clathrin-mediated endocytosis / cell-cell signaling / Clathrin-mediated endocytosis / regulation of cell shape / Potential therapeutics for SARS / cytoskeleton / neuron projection / focal adhesion / apoptotic process / ubiquitin protein ligase binding / synapse / plasma membrane / cytoplasm / cytosol
Similarity search - Function
SH3 domain-containing kinase-binding protein 1, first SH3 domain / SH3 domain-containing kinase-binding protein 1, second SH3 domain / SH3 domain-containing kinase-binding protein 1, third SH3 domain / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
SH3 domain-containing kinase-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å
AuthorsWong, L. / Habeck, M. / Griesinger, C. / Becker, S.
CitationJournal: Sci.Signal. / Year: 2016
Title: The Adaptor Protein Cin85 Assembles Intracellular Signaling Clusters for B Cell Activation.
Authors: Kuhn, J. / Wong, L.E. / Pirkuliyeva, S. / Schulz, K. / Schwiegk, C. / Funfgeld, K.G. / Keppler, S. / Batista, F.D. / Urlaub, H. / Habeck, M. / Becker, S. / Griesinger, C. / Wienands, J.
History
DepositionAug 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.2Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1475
Polymers7,8861
Non-polymers2624
Water25214
1
A: SH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1
hetero molecules

A: SH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1
hetero molecules

A: SH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,44215
Polymers23,6573
Non-polymers78512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area7060 Å2
ΔGint-168.3 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.968, 40.968, 90.036
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1003-

ZN

21A-1004-

ZN

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Components

#1: Protein SH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1 / CD2-BINDING PROTEIN 3 / CD2BP3 / CBL-INTERACTING PROTEIN OF 85 KDA / HUMAN SRC FAMILY KINASE- ...CD2-BINDING PROTEIN 3 / CD2BP3 / CBL-INTERACTING PROTEIN OF 85 KDA / HUMAN SRC FAMILY KINASE-BINDING PROTEIN 1 / HSB-1


Mass: 7885.649 Da / Num. of mol.: 1 / Fragment: COILED-COIL DOMAIN, RESIDUES 599-662
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96B97
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL GH IS DUE TO CLONING

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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: 2.82 Å3/Da / Density % sol: 56.4 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05M ZN ACETATE, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.214
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.214 Å / Relative weight: 1
ReflectionResolution: 1.74→45.02 Å / Num. obs: 9541 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 17.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.48
Reflection shellResolution: 1.74→1.83 Å / Redundancy: 16.88 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.09 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
SADABSdata scaling
SHELXCDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.74→45.02 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.897 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28327 993 10.4 %RANDOM
Rwork0.24397 ---
obs0.24796 8537 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.917 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20.84 Å20 Å2
2--1.68 Å20 Å2
3----5.46 Å2
Refinement stepCycle: LAST / Resolution: 1.74→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms520 0 4 14 538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019539
X-RAY DIFFRACTIONr_bond_other_d0.0010.02549
X-RAY DIFFRACTIONr_angle_refined_deg1.9262.031723
X-RAY DIFFRACTIONr_angle_other_deg1.04831262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.697569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19524.825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92415106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.755156
X-RAY DIFFRACTIONr_chiral_restr0.1130.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02608
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02108
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4473.909273
X-RAY DIFFRACTIONr_mcbond_other3.4463.9272
X-RAY DIFFRACTIONr_mcangle_it4.3685.818343
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.5584.772266
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 1.738→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 76 -
Rwork0.472 603 -
obs--98.84 %

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