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- PDB-2yvr: Crystal structure of MS1043 -

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Basic information

Entry
Database: PDB / ID: 2yvr
TitleCrystal structure of MS1043
ComponentsTranscription intermediary factor 1-beta
KeywordsMETAL BINDING PROTEIN / zf-B_box domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Krueppel-associated box domain binding / SUMO ligase activity / chromo shadow domain binding / suppression of viral release by host / Generic Transcription Pathway / SUMO transferase activity / chromatin-protein adaptor activity / DNA methylation-dependent constitutive heterochromatin formation / epithelial to mesenchymal transition / protein sumoylation ...Krueppel-associated box domain binding / SUMO ligase activity / chromo shadow domain binding / suppression of viral release by host / Generic Transcription Pathway / SUMO transferase activity / chromatin-protein adaptor activity / DNA methylation-dependent constitutive heterochromatin formation / epithelial to mesenchymal transition / protein sumoylation / positive regulation of type I interferon production / heterochromatin / SUMOylation of transcription cofactors / negative regulation of canonical NF-kappaB signal transduction / positive regulation of DNA repair / Regulation of endogenous retroelements by KRAB-ZFP proteins / promoter-specific chromatin binding / euchromatin / positive regulation of protein import into nucleus / RNA polymerase II transcription regulator complex / RING-type E3 ubiquitin transferase / HCMV Early Events / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / chromatin organization / proteasome-mediated ubiquitin-dependent protein catabolic process / protein kinase activity / transcription coactivator activity / protein ubiquitination / innate immune response / negative regulation of DNA-templated transcription / DNA repair / chromatin binding / ubiquitin protein ligase binding / DNA damage response / positive regulation of DNA-templated transcription / chromatin / protein-containing complex / DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / zinc ion binding / nucleus
Similarity search - Function
Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / B-box, C-terminal / B-Box C-terminal domain / Classic Zinc Finger / B-box zinc finger / B-Box-type zinc finger ...Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / B-box, C-terminal / B-Box C-terminal domain / Classic Zinc Finger / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Double Stranded RNA Binding Domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription intermediary factor 1-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsWang, H. / Kishishita, S. / Murayama, K. / Takemoto, C. / Terada, T. / Shirouzu, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of MS1043
Authors: Wang, H. / Kishishita, S. / Takemoto, C. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionApr 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription intermediary factor 1-beta
B: Transcription intermediary factor 1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1576
Polymers11,8952
Non-polymers2624
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-12 kcal/mol
Surface area6450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.950, 38.950, 125.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein/peptide Transcription intermediary factor 1-beta / MS1043 / TIF1-beta / Tripartite motif-containing protein 28 / Nuclear corepressor KAP-1 / KRAB- ...MS1043 / TIF1-beta / Tripartite motif-containing protein 28 / Nuclear corepressor KAP-1 / KRAB- associated protein 1 / KAP-1 / KRAB-interacting protein 1 / KRIP-1 / RING finger protein 96


Mass: 5947.656 Da / Num. of mol.: 2 / Fragment: zf-B_box domain, residues in database 201-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: PK050725-03 / References: UniProt: Q13263
#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.: 95 / 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: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: HEPES, PEG4000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.2820, 1.2831
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 20, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2821
21.28311
ReflectionResolution: 1.8→50 Å / Num. obs: 9725 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Biso Wilson estimate: 14.9 Å2 / Rsym value: 0.087 / Net I/σ(I): 29.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 15.4 % / Mean I/σ(I) obs: 10.5 / Num. unique all: 940 / Rsym value: 0.274 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→33.12 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 110698.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 499 5.3 %RANDOM
Rwork0.187 ---
obs0.187 9403 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.447 Å2 / ksol: 0.392125 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å20 Å2
2--1.88 Å20 Å2
3----3.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms742 0 4 95 841
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.243 71 4.8 %
Rwork0.196 1397 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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