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- PDB-5fb0: Crystal Structure of a PHD finger bound to histone H3 T3ph peptide -

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Basic information

Entry
Database: PDB / ID: 5fb0
TitleCrystal Structure of a PHD finger bound to histone H3 T3ph peptide
Components
  • Nuclear autoantigen Sp-100
  • Peptide from Histone H3
KeywordsTRANSCRIPTION/STRUCTURAL PROTEIN / zinc finger protein / bromodomain / TRANSCRIPTION-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / negative regulation of DNA binding / type I interferon-mediated signaling pathway ...regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / negative regulation of DNA binding / type I interferon-mediated signaling pathway / response to type II interferon / type II interferon-mediated signaling pathway / regulation of angiogenesis / response to retinoic acid / SUMOylation of DNA damage response and repair proteins / Chromatin modifying enzymes / retinoic acid receptor signaling pathway / telomere organization / telomere maintenance / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / response to cytokine / Assembly of the ORC complex at the origin of replication / nuclear periphery / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA damage response, signal transduction by p53 class mediator / DNA methylation / Condensation of Prophase Chromosomes / positive regulation of DNA-binding transcription factor activity / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / negative regulation of DNA-binding transcription factor activity / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / PML body / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / kinase binding / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / Interferon gamma signaling / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / Estrogen-dependent gene expression / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / nuclear body / cadherin binding / protein domain specific binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm
Similarity search - Function
HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain ...HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain / 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 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Bromodomain-like / Histone Acetyltransferase; Chain A / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Histone H3 / Nuclear autoantigen Sp-100 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.702 Å
AuthorsLi, H. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
Major State Basic Research Development Program2015CB910503 China
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Multifaceted Histone H3 Methylation and Phosphorylation Readout by the Plant Homeodomain Finger of Human Nuclear Antigen Sp100C
Authors: Zhang, X. / Zhao, D. / Xiong, X. / He, Z. / Li, H.
History
DepositionDec 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear autoantigen Sp-100
D: Peptide from Histone H3
C: Nuclear autoantigen Sp-100
F: Peptide from Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2578
Polymers46,9954
Non-polymers2624
Water43224
1
A: Nuclear autoantigen Sp-100
D: Peptide from Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6284
Polymers23,4982
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-3 kcal/mol
Surface area10920 Å2
MethodPISA
2
C: Nuclear autoantigen Sp-100
F: Peptide from Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6284
Polymers23,4982
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-3 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.830, 99.160, 53.716
Angle α, β, γ (deg.)90.000, 93.170, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 695:719 or (resid 720 and (name...
21(chain C and (resseq 695:719 or (resid 720 and (name...
12chain F
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERTHRTHR(chain A and (resseq 695:719 or (resid 720 and (name...AA695 - 7191 - 25
121CYSCYSCYSCYS(chain A and (resseq 695:719 or (resid 720 and (name...AA72026
131SERSERTHRTHR(chain A and (resseq 695:719 or (resid 720 and (name...AA695 - 8771 - 183
141SERSERTHRTHR(chain A and (resseq 695:719 or (resid 720 and (name...AA695 - 8771 - 183
151SERSERTHRTHR(chain A and (resseq 695:719 or (resid 720 and (name...AA695 - 8771 - 183
211SERSERTHRTHR(chain C and (resseq 695:719 or (resid 720 and (name...CC695 - 7191 - 25
221CYSCYSCYSCYS(chain C and (resseq 695:719 or (resid 720 and (name...CC72026
231SERSERGLUGLU(chain C and (resseq 695:719 or (resid 720 and (name...CC695 - 8761 - 182
241SERSERGLUGLU(chain C and (resseq 695:719 or (resid 720 and (name...CC695 - 8761 - 182
251SERSERGLUGLU(chain C and (resseq 695:719 or (resid 720 and (name...CC695 - 8761 - 182
112ALAALASERSERchain FFD1 - 101 - 10
212ALAALASERSERchain DDB1 - 101 - 10

NCS ensembles :
ID
1
2

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Components

#1: Protein Nuclear autoantigen Sp-100 / SP100 nuclear antigen


Mass: 21851.764 Da / Num. of mol.: 2 / Fragment: UNP residues 696-878 / Mutation: C754S/L772Q/C793S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SP100 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23497
#2: Protein/peptide Peptide from Histone H3


Mass: 1645.777 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: chemically synthesized H3 peptide 1-15 with T3ph modification
Source: (synth.) Homo sapiens (human) / References: UniProt: K7EMV3, UniProt: P68431*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2015 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 12044 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 42.21 Å2 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.064 / Rrim(I) all: 0.151 / Χ2: 1.833 / Net I/av σ(I): 19.083 / Net I/σ(I): 7.5 / Num. measured all: 67541
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.755.70.7255860.8750.3360.81.466100
2.75-2.85.60.6455970.8570.30.7121.52199.8
2.8-2.855.70.6316050.8830.2920.6961.417100
2.85-2.915.70.575880.9050.2650.631.44100
2.91-2.975.70.526100.9240.2410.5741.533100
2.97-3.045.60.435970.9440.20.4761.55699.8
3.04-3.125.70.3425980.9710.1580.3781.527100
3.12-3.25.60.3075970.9640.1430.3391.543100
3.2-3.35.70.2676040.970.1230.2941.62999.8
3.3-3.45.70.1996050.9860.0920.221.653100
3.4-3.525.60.1685990.9880.0780.1861.694100
3.52-3.665.70.1325950.9930.0610.1461.89100
3.66-3.835.60.1166170.9940.0550.1292.155100
3.83-4.035.60.1115930.9940.0520.1232.18299.8
4.03-4.295.50.1016010.9950.0480.1122.31999.8
4.29-4.625.40.0846100.9950.040.0932.35299.8
4.62-5.085.50.0756010.9960.0350.0822.232100
5.08-5.815.40.0716130.9960.0340.0791.87599.8
5.81-7.325.70.0696090.9970.0320.0761.959100
7.32-505.40.0566190.9960.0260.0622.78898.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.10_2155: ???refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.702→32.143 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2761 1238 10.29 %
Rwork0.2236 10794 -
obs0.2289 12032 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.65 Å2 / Biso mean: 59.0318 Å2 / Biso min: 15.63 Å2
Refinement stepCycle: final / Resolution: 2.702→32.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 4 24 3043
Biso mean--38.91 48.99 -
Num. residues----362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033083
X-RAY DIFFRACTIONf_angle_d0.6354138
X-RAY DIFFRACTIONf_chiral_restr0.04423
X-RAY DIFFRACTIONf_plane_restr0.006538
X-RAY DIFFRACTIONf_dihedral_angle_d19.6451884
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1549X-RAY DIFFRACTION5.182TORSIONAL
12C1549X-RAY DIFFRACTION5.182TORSIONAL
21F92X-RAY DIFFRACTION5.182TORSIONAL
22D92X-RAY DIFFRACTION5.182TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7022-2.81040.3871360.286611731309
2.8104-2.93820.3491720.281311601332
2.9382-3.0930.34011390.253912071346
3.093-3.28660.29831170.256512001317
3.2866-3.540.28671160.235612181334
3.54-3.89570.26831320.200912101342
3.8957-4.45820.24051550.201511791334
4.4582-5.6120.26331580.210611851343
5.612-32.14570.23481130.20512621375
Refinement TLS params.Method: refined / Origin x: 19.7922 Å / Origin y: -16.0057 Å / Origin z: 13.4019 Å
111213212223313233
T0.2324 Å2-0.0571 Å2-0.0029 Å2-0.2494 Å2-0.0132 Å2--0.2144 Å2
L-0.2409 °2-0.1344 °20.0378 °2-1.3103 °2-0.6822 °2---1.032 °2
S-0.0484 Å °-0.0439 Å °-0.002 Å °0.0061 Å °-0.0158 Å °-0.0719 Å °-0.0068 Å °0.232 Å °-0.0172 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA695 - 877
2X-RAY DIFFRACTION1allB5 - 8
3X-RAY DIFFRACTION1allD1 - 10
4X-RAY DIFFRACTION1allC695 - 876
5X-RAY DIFFRACTION1allF1 - 10
6X-RAY DIFFRACTION1allS1 - 24

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