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- PDB-4go6: Crystal structure of HCF-1 self-association sequence 1 -

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Basic information

Entry
Database: PDB / ID: 4go6
TitleCrystal structure of HCF-1 self-association sequence 1
Components
  • HCF C-terminal chain 1
  • HCF N-terminal chain 1
KeywordsPROTEIN BINDING / Tandem Fibronectin repeat / protein interaction / TRANSCRIPTION
Function / homology
Function and homology information


release from viral latency / blastocyst hatching / Set1C/COMPASS complex / MLL1/2 complex / NSL complex / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / MLL1 complex / histone acetyltransferase complex / regulation of protein-containing complex assembly ...release from viral latency / blastocyst hatching / Set1C/COMPASS complex / MLL1/2 complex / NSL complex / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / MLL1 complex / histone acetyltransferase complex / regulation of protein-containing complex assembly / positive regulation of cell cycle / Transcriptional activation of mitochondrial biogenesis / chromatin DNA binding / UCH proteinases / HATs acetylate histones / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / transcription coactivator activity / protein stabilization / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / neuronal cell body / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2590 / Host cell factor / Host cell factor, Kelch-repeats domain / Kelch-type beta propeller / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2590 / Host cell factor / Host cell factor, Kelch-repeats domain / Kelch-type beta propeller / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Special / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsPark, J. / Lammers, F. / Herr, W. / Song, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: HCF-1 self-association via an interdigitated Fn3 structure facilitates transcriptional regulatory complex formation
Authors: Park, J. / Lammers, F. / Herr, W. / Song, J.
History
DepositionAug 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: HCF N-terminal chain 1
B: HCF C-terminal chain 1
C: HCF N-terminal chain 1
D: HCF C-terminal chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6798
Polymers60,2954
Non-polymers3844
Water59433
1
A: HCF N-terminal chain 1
B: HCF C-terminal chain 1
C: HCF N-terminal chain 1
D: HCF C-terminal chain 1
hetero molecules

A: HCF N-terminal chain 1
B: HCF C-terminal chain 1
C: HCF N-terminal chain 1
D: HCF C-terminal chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,35816
Polymers120,5898
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area27620 Å2
ΔGint-253 kcal/mol
Surface area38220 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-121 kcal/mol
Surface area20150 Å2
MethodPISA
3
A: HCF N-terminal chain 1
B: HCF C-terminal chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3394
Polymers30,1472
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-48 kcal/mol
Surface area11130 Å2
MethodPISA
4
C: HCF N-terminal chain 1
D: HCF C-terminal chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3394
Polymers30,1472
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-56 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.899, 183.512, 86.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN.

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Components

#1: Protein/peptide HCF N-terminal chain 1 / HCF / HCF-1 / C1 factor / CFF / VCAF / VP16 accessory protein / HCF N-terminal chain 2 / HCF N- ...HCF / HCF-1 / C1 factor / CFF / VCAF / VP16 accessory protein / HCF N-terminal chain 2 / HCF N-terminal chain 3 / HCF N-terminal chain 4 / HCF N-terminal chain 5 / HCF N-terminal chain 6


Mass: 4918.472 Da / Num. of mol.: 2 / Fragment: HCF-1 SAS1N, UNP residues 360-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Homo sapiens / Plasmid: pET21a, pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P51610
#2: Protein HCF C-terminal chain 1 / HCF / HCF-1 / C1 factor / CFF / VCAF / VP16 accessory protein / HCF C-terminal chain 2 / HCF C- ...HCF / HCF-1 / C1 factor / CFF / VCAF / VP16 accessory protein / HCF C-terminal chain 2 / HCF C-terminal chain 3 / HCF C-terminal chain 4 / HCF C-terminal chain 5 / HCF C-terminal chain 6


Mass: 25228.830 Da / Num. of mol.: 2 / Fragment: HCF-1 SAS1C-NLS, UNP residues 1806-2035
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCFC1, HCF1, HFC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P51610
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.14 Å3/Da / Density % sol: 60.83 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.23M ammonium sulfate, 5% Isopropanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 42424 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 59.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 31.3
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 3.88 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→19.94 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED IN PHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1894 4.7 %random
Rwork0.231 ---
all-40205 --
obs-37625 93.6 %-
Solvent computationBsol: 36.6369 Å2
Displacement parametersBiso max: 172.37 Å2 / Biso mean: 58.2096 Å2 / Biso min: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1-36.282 Å20 Å20 Å2
2---16.83 Å20 Å2
3----19.451 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.62 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 20 33 3295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.426 299 -
Rwork0.392 --
obs-5171 81.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3sul.param

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