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- PDB-4kha: Structural basis of histone H2A-H2B recognition by the essential ... -

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Basic information

Entry
Database: PDB / ID: 4kha
TitleStructural basis of histone H2A-H2B recognition by the essential chaperone FACT
Components
  • Histone H2A
  • Spt16M-Histone H2B 1.1 chimera
KeywordsCHAPERONE/NUCLEAR PROTEIN / tandem PHL / Pleckstrin-homology like / U-turn motif / Histone Chaperone / chromatin / transcription / Histones / Nucleus / CHAPERONE-NUCLEAR PROTEIN complex
Function / homology
Function and homology information


FACT complex / nucleosome organization / nucleosome binding / transcription elongation by RNA polymerase II / structural constituent of chromatin / heterochromatin formation / nucleosome / regulation of gene expression / DNA replication / protein heterodimerization activity ...FACT complex / nucleosome organization / nucleosome binding / transcription elongation by RNA polymerase II / structural constituent of chromatin / heterochromatin formation / nucleosome / regulation of gene expression / DNA replication / protein heterodimerization activity / DNA repair / DNA binding / metal ion binding / nucleus
Similarity search - Function
PH-domain like - #150 / FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / : / FACT complex subunit SPT16 PH-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain ...PH-domain like - #150 / FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / : / FACT complex subunit SPT16 PH-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Creatinase/Aminopeptidase P/Spt16, N-terminal / Histone, subunit A / Histone, subunit A / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / PH-like domain superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FACT complex subunit / Histone H2B 1.1 / Histone H2A
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum (fungus)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHondele, M. / Halbach, F. / Hassler, M. / Ladurner, A.G.
CitationJournal: Nature / Year: 2013
Title: Structural basis of histone H2A-H2B recognition by the essential chaperone FACT.
Authors: Hondele, M. / Stuwe, T. / Hassler, M. / Halbach, F. / Bowman, A. / Zhang, E.T. / Nijmeijer, B. / Kotthoff, C. / Rybin, V. / Amlacher, S. / Hurt, E. / Ladurner, A.G.
History
DepositionApr 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Derived calculations
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Jul 10, 2013Group: Database references
Revision 1.4Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spt16M-Histone H2B 1.1 chimera
B: Histone H2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1015
Polymers56,9082
Non-polymers1933
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-67 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.421, 108.421, 117.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1357-

HOH

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Components

#1: Protein Spt16M-Histone H2B 1.1 chimera / H2B1.1


Mass: 46745.031 Da / Num. of mol.: 1 / Fragment: UNP residues 652-945 and 34-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum (fungus), (gene. exp.) Xenopus laevis (African clawed frog)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0052370, CTHT_0052370 / Plasmid: pETM-CN-His (Amp) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPLUS(DE3)-RIL / References: UniProt: G0SDN1, UniProt: P02281
#2: Protein Histone H2A


Mass: 10162.794 Da / Num. of mol.: 1 / Fragment: UNP residues 15-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Plasmid: pETM-CN untagged (Kan) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPLUS(DE3)-RIL / References: UniProt: Q6AZJ8
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: manual setup 1ul protein (15 mg / ml) plus 1 ul crystallization buffer (7.25% [vol/vol] PEG8000, 0.2 M MgCl2, 0.1 M Tris pH 7.8), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2011 / Details: mirrors
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.3→46.7 Å / Num. obs: 31867 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1.9 / Redundancy: 8.8 % / Biso Wilson estimate: 51.797 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 9 % / Rmerge(I) obs: 0.01096 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPPhaserphasing
PHENIXRefinerefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→46.699 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1505 5.04 %
Rwork0.1908 --
obs0.1927 29835 99.9 %
all-31828 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.75 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3411 0 10 116 3537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063486
X-RAY DIFFRACTIONf_angle_d0.8964749
X-RAY DIFFRACTIONf_dihedral_angle_d14.1851228
X-RAY DIFFRACTIONf_chiral_restr0.053562
X-RAY DIFFRACTIONf_plane_restr0.004614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.42590.30251270.26372530X-RAY DIFFRACTION100
2.4259-2.51260.30361180.2432543X-RAY DIFFRACTION100
2.5126-2.61320.26031260.23452540X-RAY DIFFRACTION100
2.6132-2.73210.2661370.22472534X-RAY DIFFRACTION100
2.7321-2.87610.25661250.22382549X-RAY DIFFRACTION100
2.8761-3.05630.25621390.22322542X-RAY DIFFRACTION100
3.0563-3.29220.30651480.21462558X-RAY DIFFRACTION100
3.2922-3.62340.23641400.19582568X-RAY DIFFRACTION100
3.6234-4.14740.24131530.17392573X-RAY DIFFRACTION100
4.1474-5.22420.16521390.15092637X-RAY DIFFRACTION100
5.2242-46.70860.19761530.1842756X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.9758-0.7352-3.11172.2471-0.3033.7946-0.04790.44390.70850.1408-0.30940.6529-0.3975-0.6789-0.38650.9239-0.08740.3090.68180.54720.91412.4348-14.272-19.5974
20.0236-0.01980.0140.03170.05270.2178-0.8882.2318-0.1334-1.47220.7176-0.7723-0.01370.67150.15021.2019-0.32460.05380.98790.21031.241420.2829-7.8788-21.9824
35.93351.8711-1.22725.402-0.42322.70070.03180.0668-0.01930.0006-0.4147-0.2425-0.80680.89090.07330.6924-0.36350.08750.65530.09920.55922.1438-24.0169-18.8317
40.20980.1779-0.23180.3796-0.51820.67090.43110.228-0.2204-0.6051-0.8536-0.1920.9169-0.45590.0390.9065-0.03740.05310.93080.18410.505410.4071-31.775-21.1413
54.17760.3109-0.96342.1467-0.03726.2041-0.07570.28820.1295-0.35920.1956-0.2392-0.28560.306-0.05910.6984-0.20840.12260.74960.09320.546517.7311-22.4952-22.0537
60.0709-0.0149-0.48210.00110.08863.27920.23921.09470.5468-1.0189-0.2419-0.67030.0818-0.3103-0.44950.5408-0.64170.47511.28470.3676-0.040415.2291-23.7095-31.8602
74.12870.4555-2.1673.72410.19295.4923-0.14680.1552-0.1483-0.25070.1053-0.1036-0.41610.06640.13590.4922-0.13180.05650.59930.15480.45710.9902-25.1519-12.6296
84.959-1.90945.27590.7258-2.0515.63930.68481.2905-0.5891-0.6213-0.494-0.04670.27890.0318-0.72070.69180.1037-0.02121.24840.16790.833127.9599-37.264-11.9393
95.16541.0267-1.21421.4508-0.31997.1180.1195-0.1350.22940.0434-0.0979-0.2762-1.10051.3626-0.09270.6467-0.31150.03820.84150.05160.522420.6376-21.8313-5.8832
106.29522.722-0.16364.83170.83995.2233-0.2404-0.1872-0.5547-0.1340.2027-0.5828-0.32330.72670.05920.3902-0.03590.03770.57470.12160.48598.8137-35.8542-1.7472
113.37480.7018-0.72832.18150.9882.8150.0566-0.1276-0.05510.0408-0.08-0.1349-0.24440.00110.07330.3590.0345-0.04430.39090.05560.2541-6.7867-34.77135.9417
120.080.0232-0.03540.1374-0.15290.10270.58120.0229-0.33510.4184-0.19950.3597-0.44840.03260.52670.74490.0208-0.06560.7174-0.05310.7053-11.9935-45.238610.8751
131.30721.59810.52315.81381.36053.6992-0.1389-0.2179-0.10090.41040.1964-0.0419-0.0276-0.3-0.00940.25930.05160.02010.50520.0640.2794-24.4918-44.76768.5126
143.53381.1670.15946.82771.04876.55390.30330.134-0.8-0.1455-0.10480.66640.8823-0.88270.01870.4423-0.1391-0.0540.462-0.02020.6111-31.8084-63.7949-0.6463
157.7933-2.327-2.57090.71610.9712.439-0.17331.0722-0.7655-0.0188-0.38240.02160.35790.56240.70330.2196-0.69631.20050.7449-0.10270.974-40.4428-53.796911.3867
164.76980.61470.25157.48931.73720.450.01250.13670.0736-0.28180.12611.0107-0.3549-1.41120.1020.3214-0.0103-0.02130.6477-0.01620.6186-38.1165-49.2014-4.258
172.3364-1.1847-1.78424.98482.03591.67370.16690.1580.3654-0.97260.01420.0818-0.175-0.1429-0.35520.47150.0809-0.0430.45890.00220.3308-26.4836-43.0759-7.8618
186.12874.4843.74514.55261.2743.9418-0.03970.5954-0.3727-0.5459-0.1731-1.34550.62680.91770.15570.34660.01410.00680.3584-0.0480.4189-19.7893-54.4216-4.8315
197.38954.26133.25543.42680.93752.36860.54530.2041-1.18170.05020.0633-0.53321.40220.7008-0.32530.57370.0599-0.0370.4931-0.03730.5243-19.1799-61.765-4.7401
202.4925-0.999-0.3816.99124.653.20960.00340.1021-0.1269-0.1612-0.15680.5556-0.0368-0.53820.41790.37970.00310.01270.50110.04580.4079-30.1783-51.2629-0.7741
212.9686-0.1356-0.56545.92785.88025.91230.1808-0.42760.47850.2289-0.16751.7085-0.7629-1.14440.79610.45920.14630.08170.56720.04140.3975-33.6206-41.016714.155
228.11723.0457-1.45152.86821.35242.3555-0.529-1.1890.11541.1755-0.61.5145-0.5522-0.99130.6830.68620.26510.06110.97050.09180.462-33.7391-33.322121.5495
233.69470.31520.48257.9564.85832.96520.3272-0.69610.47970.1811-0.23170.4717-0.8359-0.0205-0.03020.54080.15120.04410.5523-0.07120.2992-26.5532-31.834220.6744
242.4295-3.8652-3.82026.29346.14726.01410.0340.00710.33411.7967-0.4055-0.01420.79370.70730.31240.660.23110.00340.8413-0.02690.3963-27.3839-41.640323.3591
250.8521.2547-0.43448.42733.84498.4511-0.154-0.33720.36591.161-0.19480.85830.9501-0.66750.25420.6731-0.03950.15040.6960.1070.5832-33.8262-50.947918.9246
262.126-3.7168-3.65566.68386.64146.61140.49630.8072-1.31611.56920.8542-1.8362.3181.3453-1.39871.01520.15310.02181.3602-0.13320.91-23.1527-48.829524.0348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 649 through 656 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 657 through 662 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 663 through 672 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 673 through 677 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 678 through 697 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 698 through 701 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 702 through 748 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 749 through 783 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 784 through 816 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 817 through 848 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 849 through 940 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 941 through 1031 )A0
13X-RAY DIFFRACTION13chain 'A' and (resid 1032 through 1075 )A0
14X-RAY DIFFRACTION14chain 'A' and (resid 1076 through 1099 )A0
15X-RAY DIFFRACTION15chain 'A' and (resid 1100 through 1103 )A0
16X-RAY DIFFRACTION16chain 'A' and (resid 1104 through 1121 )A0
17X-RAY DIFFRACTION17chain 'B' and (resid 11 through 30 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 31 through 34 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 35 through 41 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 42 through 60 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 61 through 67 )B0
22X-RAY DIFFRACTION22chain 'B' and (resid 68 through 73 )B0
23X-RAY DIFFRACTION23chain 'B' and (resid 74 through 79 )B0
24X-RAY DIFFRACTION24chain 'B' and (resid 80 through 85 )B0
25X-RAY DIFFRACTION25chain 'B' and (resid 86 through 98 )B0
26X-RAY DIFFRACTION26chain 'B' and (resid 99 through 102 )B0

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