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- PDB-2v6c: Crystal structure of ErbB3 binding protein 1 (Ebp1) -

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Basic information

Entry
Database: PDB / ID: 2v6c
TitleCrystal structure of ErbB3 binding protein 1 (Ebp1)
ComponentsPROLIFERATION-ASSOCIATED PROTEIN 2G4
KeywordsTRANSCRIPTION REGULATOR / TRANSLATION REGULATION / TRANSLATIONAL REGULATOR / RNA-BINDING / ACETYLATION / RNA BINDING / TRANSCRIPTION / COBALT / NUCLEUS / REPRESSOR / HYDROLASE / CYTOPLASM / TRANSCRIPTION REGULATION / PHOSPHORYLATION / RRNA PROCESSING / RIBONUCLEOPROTEIN
Function / homology
Function and homology information


Neutrophil degranulation / positive regulation of cell differentiation / rRNA processing / transcription corepressor activity / regulation of translation / nucleic acid binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus ...Neutrophil degranulation / positive regulation of cell differentiation / rRNA processing / transcription corepressor activity / regulation of translation / nucleic acid binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / negative regulation of apoptotic process / RNA binding / nucleus / cytoplasm
Similarity search - Function
PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Proliferation-associated protein 2G4
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMonie, T.P. / Perrin, A.J. / Birtley, J.R. / Curry, S.
CitationJournal: Embo J. / Year: 2007
Title: Structural Insights Into the Transcriptional and Translational Roles of Ebp1
Authors: Monie, T.P. / Perrin, A.J. / Birtley, J.R. / Sweeney, T.R. / Karakasiliotis, I. / Chaudry, Y. / Roberts, L.O. / Matthews, S. / Goodfellow, I.G. / Curry, S.
History
DepositionJul 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROLIFERATION-ASSOCIATED PROTEIN 2G4


Theoretical massNumber of molelcules
Total (without water)39,3871
Polymers39,3871
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.147, 72.779, 115.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROLIFERATION-ASSOCIATED PROTEIN 2G4 / ERBB3 BINDING PROTEIN 1 / PROLIFERATION-ASSOCIATED PROTEIN 1 / PROTEIN P38-2G4 / MPP1 / IRES- ...ERBB3 BINDING PROTEIN 1 / PROLIFERATION-ASSOCIATED PROTEIN 1 / PROTEIN P38-2G4 / MPP1 / IRES-SPECIFIC CELLULAR TRANS-ACTING FACTOR 45 KDA / ITAF45


Mass: 39387.074 Da / Num. of mol.: 1 / Fragment: RESIDUES 7-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA (NOVAGEN) / References: UniProt: P50580
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMAY PLAY A ROLE IN A ERBB3-REGULATED SIGNAL TRANSDUCTION PATHWAY
Sequence detailsSEQUENCE CONTAINS 2 MUTATIONS (T279A, K311R) WHICH HAVE BEEN NOTED IN THE LITERATURE AS A PROBABLE ...SEQUENCE CONTAINS 2 MUTATIONS (T279A, K311R) WHICH HAVE BEEN NOTED IN THE LITERATURE AS A PROBABLE POLYMORPHISM

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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: 2.63 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 7.7 / Details: SEE PAPER, pH 7.7

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 15, 2005 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.5→38.4 Å / Num. obs: 14714 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.3 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASER1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1KQ9 AND 1XGS

1kq9

1xgs


Resolution: 2.5→37.45 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1282714.16 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: RESIDUES 1-8 AND 361-394 WERE MISSING FROM THE PROTEIN USED IN CRYSALLISATION. RESIDUE 8 WAS MUTATED TO GLU BY THE CLONING PROCEDURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 735 5 %RANDOM
Rwork0.182 ---
obs0.182 14714 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.1966 Å2 / ksol: 0.288707 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.8 Å20 Å20 Å2
2---2.46 Å20 Å2
3---6.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 0 55 2784
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 134 5.6 %
Rwork0.262 2256 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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