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- PDB-6l34: Crystal structure of the HMG domain of human FACT complex subunit... -

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Basic information

Entry
Database: PDB / ID: 6l34
TitleCrystal structure of the HMG domain of human FACT complex subunit SSRP1
ComponentsFACT complex subunit SSRP1
KeywordsCHAPERONE / Histone chaperone
Function / homology
Function and homology information


FACT complex / regulation of chromatin organization / nucleosome disassembly / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat ...FACT complex / regulation of chromatin organization / nucleosome disassembly / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / nucleosome binding / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / nucleosome assembly / histone binding / DNA replication / Regulation of TP53 Activity through Phosphorylation / DNA repair / nucleolus / DNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
: / FACT complex subunit SSRP1, C-terminal domain / : / SSRP1 PH domain / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / Structure-specific recognition protein (SSRP1) / POB3-like N-terminal PH domain ...: / FACT complex subunit SSRP1, C-terminal domain / : / SSRP1 PH domain / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / Structure-specific recognition protein (SSRP1) / POB3-like N-terminal PH domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
FACT complex subunit SSRP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 Å
AuthorsLi, H.Y. / Hu, T.T. / Dou, Y.S. / Su, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370735 China
CitationJournal: To Be Published
Title: Crystal structure of the HMG domain of human FACT complex subunit SSRP1
Authors: Li, H.Y. / Hu, T.T. / Dou, Y.S. / Su, D.
History
DepositionOct 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FACT complex subunit SSRP1


Theoretical massNumber of molelcules
Total (without water)8,1241
Polymers8,1241
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5590 Å2
Unit cell
Length a, b, c (Å)64.985, 64.985, 55.074
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

21A-673-

HOH

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Components

#1: Protein FACT complex subunit SSRP1 / Chromatin-specific transcription elongation factor 80 kDa subunit / Facilitates chromatin ...Chromatin-specific transcription elongation factor 80 kDa subunit / Facilitates chromatin transcription complex 80 kDa subunit / FACTp80 / Facilitates chromatin transcription complex subunit SSRP1 / Recombination signal sequence recognition protein 1 / Structure-specific recognition protein 1 / hSSRP1 / T160


Mass: 8124.314 Da / Num. of mol.: 1 / Fragment: HMG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SSRP1, FACT80 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08945
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 4.13 Å3/Da / Density % sol: 70.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2M DL-malic acid PH7.0, 0.1M BIS-TRIS propane pH7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.996→39.362 Å / Num. obs: 9083 / % possible obs: 99.85 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 27.4
Reflection shellResolution: 1.997→2.068 Å / Rmerge(I) obs: 0.327 / Num. unique obs: 909

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FGH

3fgh


Resolution: 1.996→39.362 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.47
RfactorNum. reflection% reflection
Rfree0.199 452 4.98 %
Rwork0.1753 --
obs0.1766 9083 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.77 Å2 / Biso mean: 28.6064 Å2 / Biso min: 16.97 Å2
Refinement stepCycle: final / Resolution: 1.996→39.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 0 0 104 671
Biso mean---36.76 -
Num. residues----68
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007578
X-RAY DIFFRACTIONf_angle_d0.729767
X-RAY DIFFRACTIONf_chiral_restr0.04173
X-RAY DIFFRACTIONf_plane_restr0.00496
X-RAY DIFFRACTIONf_dihedral_angle_d1.752365
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.996-2.28460.1971450.16892863
2.2846-2.87830.18471460.18472861
2.8783-39.3620.20571610.17112907

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