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- PDB-6kn5: Crystal structure of AFF4 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6kn5
TitleCrystal structure of AFF4 C-terminal domain
ComponentsAF4/FMR2 family member 4
KeywordsTRANSCRIPTION / AFF4 / histone acetylation
Function / homology
Function and homology information


super elongation complex / spermatid development / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / response to endoplasmic reticulum stress / transcription elongation factor complex / euchromatin / fibrillar center / regulation of gene expression / nucleoplasm
Similarity search - Function
AF-4 proto-oncoprotein N-terminal region / AF4/FMR2 family / AF4 interaction motif / AF4/FMR2, C-terminal homology domain / AF4 interaction motif / AFF4, C-terminal homology domain
Similarity search - Domain/homology
AF4/FMR2 family member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, L.J. / Yang, W.S. / Xu, R.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R61AI133697 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA211861 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R33AI122418 United States
CitationJournal: Commun Biol / Year: 2020
Title: Acetylation of histone H3K27 signals the transcriptional elongation for estrogen receptor alpha.
Authors: Gao, Y. / Chen, L. / Han, Y. / Wu, F. / Yang, W.S. / Zhang, Z. / Huo, T. / Zhu, Y. / Yu, C. / Kim, H. / Lee, M. / Tang, Z. / Phillips, K. / He, B. / Jung, S.Y. / Song, Y. / Zhu, B. / Xu, R.M. / Feng, Q.
History
DepositionAug 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AF4/FMR2 family member 4


Theoretical massNumber of molelcules
Total (without water)29,7691
Polymers29,7691
Non-polymers00
Water59433
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 area13010 Å2
Unit cell
Length a, b, c (Å)41.062, 71.117, 187.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2

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Components

#1: Protein AF4/FMR2 family member 4 / ALL1-fused gene from chromosome 5q31 protein / Protein AF-5q31 / Major CDK9 elongation factor- ...ALL1-fused gene from chromosome 5q31 protein / Protein AF-5q31 / Major CDK9 elongation factor-associated protein


Mass: 29768.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AFF4, AF5Q31, MCEF, HSPC092 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHB7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: sodium dihydrogen phosphate, potassium monohydrogen phosphate, 2-(N-morpholino)ethanesulfonic acid

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97845 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 2.2→46.94 Å / Num. obs: 14447 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 47.48 Å2 / CC1/2: 0.999 / R split: 0.028 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Net I/σ(I): 21.8
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.946 / Num. unique obs: 1249

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.935 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2923 1445 10 %
Rwork0.2475 12999 -
obs0.2518 14444 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.2 Å2 / Biso mean: 62.0095 Å2 / Biso min: 24.12 Å2
Refinement stepCycle: final / Resolution: 2.2→46.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 0 33 1862
Biso mean---54.73 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041873
X-RAY DIFFRACTIONf_angle_d0.7192525
X-RAY DIFFRACTIONf_chiral_restr0.312279
X-RAY DIFFRACTIONf_plane_restr0.004319
X-RAY DIFFRACTIONf_dihedral_angle_d25.604707
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2001-2.27870.3561440.30151299
2.2787-2.36990.3471400.28621256
2.3699-2.47780.33821400.3021266
2.4778-2.60840.31331440.29341286
2.6084-2.77180.28861420.28151279
2.7718-2.98580.29581420.27461286
2.9858-3.28620.32021460.26811304
3.2862-3.76160.28831440.24731307
3.7616-4.73850.26561470.20811313
4.7385-46.9350.2831560.23381403

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