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- PDB-6v2r: Crystal Structure of chromodomain of CBX7 mutant V13A in complex ... -

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Basic information

Entry
Database: PDB / ID: 6v2r
TitleCrystal Structure of chromodomain of CBX7 mutant V13A in complex with inhibitor UNC3866
Components
  • Chromobox protein homolog 7
  • UNC3866
KeywordsGENE REGULATION / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


PRC1 complex / PcG protein complex / chromatin organization / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Chromobox protein homolog 7 / CBX family C-terminal motif / CBX family C-terminal motif / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain ...Chromobox protein homolog 7 / CBX family C-terminal motif / CBX family C-terminal motif / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
UNC3866 / Chromobox protein homolog 7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsLiu, Y. / Tempel, W. / Walker, J.R. / Stuckey, J.I. / Dickson, B.M. / James, L.I. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...Liu, Y. / Tempel, W. / Walker, J.R. / Stuckey, J.I. / Dickson, B.M. / James, L.I. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Cell Chem Biol / Year: 2020
Title: Structural Basis for the Binding Selectivity of Human CDY Chromodomains.
Authors: Dong, C. / Liu, Y. / Lyu, T.J. / Beldar, S. / Lamb, K.N. / Tempel, W. / Li, Y. / Li, Z. / James, L.I. / Qin, S. / Wang, Y. / Min, J.
History
DepositionNov 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 7
B: UNC3866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,09819
Polymers7,5842
Non-polymers1,51517
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-7 kcal/mol
Surface area4400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.193, 40.193, 83.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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Components

#1: Protein Chromobox protein homolog 7 / CBX7


Mass: 6788.799 Da / Num. of mol.: 1 / Fragment: Chromodomain / Mutation: V13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX7 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -V2R-pRARE2 / References: UniProt: O95931
#2: Protein/peptide UNC3866


Type: Oligopeptide / Class: Inhibitor / Mass: 795.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UNC3866
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 89.093 Da / Num. of mol.: 17 / Source method: isolated from a natural source
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5 M ammonium sulfate, 0.1 M bis-tris propane, pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.57→23.46 Å / Num. obs: 10074 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 15.94 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.042 / Net I/σ(I): 43
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
8.62-23.4696.68.30.0268810.02892.9
1.57-1.610012.60.5484840.9430.5725

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: isomorphous to PDB entry 5EPJ

5epj


Resolution: 1.6→23.46 Å / SU ML: 0.1378 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.6482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 682 7.14 %
Rwork0.1928 8868 -
obs0.1957 9550 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.16 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms502 0 17 54 573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137525
X-RAY DIFFRACTIONf_angle_d1.2733712
X-RAY DIFFRACTIONf_chiral_restr0.087772
X-RAY DIFFRACTIONf_plane_restr0.010287
X-RAY DIFFRACTIONf_dihedral_angle_d22.6598197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.720.22371520.17391704X-RAY DIFFRACTION100
1.72-1.90.20311420.17841718X-RAY DIFFRACTION100
1.9-2.170.20761240.17991747X-RAY DIFFRACTION100
2.17-2.730.25331180.20351798X-RAY DIFFRACTION99.95
2.74-23.460.24781460.1981901X-RAY DIFFRACTION100
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)
14.63298593417-1.56767583889-0.09102481221836.237739607740.104279168983.39143299830.083461029470.256589509587-0.175260399488-0.254008894767-0.139830704748-0.314789034510.0533408901615-0.06168343047570.02656758031260.131311801196-0.01663911227850.01237179807710.145432359021-0.009031085381030.10294005438819.821844253529.73177534543.1045876558
22.64591539652-1.71287096125-1.416378339242.880537357311.193318567672.473228063760.04038961765220.106903486276-0.0521708073228-0.112693548204-0.1250610248350.170937179658-0.00579109404938-0.149697679920.08624580851640.1292453556640.0207961105592-0.001629752694950.1373029835740.001559539845790.13035819388314.216086414133.72544846830.77423805067
32.49988804385-0.175257934571.439344415512.86968069474-0.8117792913933.934864437370.18980666747-0.3092154529370.03815382442890.293994074349-0.03913790703170.264512333967-0.174246350578-0.478743684059-0.1405864906740.1358252252250.001037266236290.0396348974930.136488325062-0.002844935895970.13351539718412.344818648430.53689427147.4525250802
46.12943628554-1.045684646751.123989863895.04894343384-0.6370457724575.83937101734-0.1782778437950.02554298504570.8868976537970.222547617921-0.129459370721-0.0918761354904-0.674031681285-0.001073276975160.2442843020750.191143625778-0.0233003360043-0.03603336529050.16297631172-0.005216477906860.23260300568619.937231301840.313789302211.0597008247
59.922537312587.85321531933-2.728994037257.09325111444-2.865157968586.60891160029-0.106290076639-0.0434574502425-0.2566066958560.05402579790760.02696621936210.1405312898860.123705762748-0.05448258755280.06821555903210.103256325467-0.0099377511325-0.01366050996990.1077743701170.006879830638970.18936401390115.183640691825.04312207516.63967330236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 50 )
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 62 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 4 )

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