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- PDB-6r80: Structure of AFF4 C-terminal homology domain -

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Basic information

Entry
Database: PDB / ID: 6r80
TitleStructure of AFF4 C-terminal homology domain
ComponentsAF4/FMR2 family member 4
KeywordsTRANSCRIPTION / transcription elongation factor / dimerisation domain
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
AF4/FMR2 family / AF4 interaction motif / AF4/FMR2, C-terminal homology domain / AF-4 proto-oncoprotein N-terminal region / 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 / SAD / Resolution: 2.2 Å
AuthorsChen, Y. / Cramer, P.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
German Research FoundationSPP1935 Germany
European Research CouncilTRANSREGULON, No 693023 Germany
Volkswagen Foundation Germany
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structure of the super-elongation complex subunit AFF4 C-terminal homology domain reveals requirements for AFF homo- and heterodimerization.
Authors: Chen, Y. / Cramer, P.
History
DepositionMar 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: AF4/FMR2 family member 4


Theoretical massNumber of molelcules
Total (without water)32,2991
Polymers32,2991
Non-polymers00
Water75742
1
A: AF4/FMR2 family member 4

A: AF4/FMR2 family member 4


Theoretical massNumber of molelcules
Total (without water)64,5972
Polymers64,5972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Buried area3310 Å2
ΔGint-27 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.530, 79.480, 185.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-1224-

HOH

21A-1225-

HOH

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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: 32298.500 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


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.94 Å3/Da / Density % sol: 58.13 % / Description: Rod-like crystal
Crystal growTemperature: 291.15 K / Method: evaporation / Details: PEG 8000 14%-16% KH2PO4 0.04 M Glycerol 20% / PH range: 5.8-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 16107 / % possible obs: 100 % / Redundancy: 6.97 % / CC1/2: 0.999 / Net I/σ(I): 11.04
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.85 % / Mean I/σ(I) obs: 1.11 / Num. unique obs: 2204 / CC1/2: 0.663 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSVERSION Nov 11, 2017data reduction
XSCALEVERSION Jan 26, 2018data scaling
HKL2MapVersion 0.4.e-betaphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.36 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.04
Details: Refinement strategy --xyz --individual B-factors --TLS refinement --Occupancies(occupancies of SE sites) 5 cycles Targets and weighting --Target function ML --optimise x-ray/stereochemistry ...Details: Refinement strategy --xyz --individual B-factors --TLS refinement --Occupancies(occupancies of SE sites) 5 cycles Targets and weighting --Target function ML --optimise x-ray/stereochemistry weight --optimise x-ray/ADP weight other options --Automatically correct N/Q/H errors --Update waters
RfactorNum. reflection% reflection
Rfree0.2515 802 4.99 %
Rwork0.2323 --
obs0.2334 16066 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 0 42 1853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021846
X-RAY DIFFRACTIONf_angle_d0.462489
X-RAY DIFFRACTIONf_dihedral_angle_d11.231129
X-RAY DIFFRACTIONf_chiral_restr0.032279
X-RAY DIFFRACTIONf_plane_restr0.003312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.33790.43931290.44142494X-RAY DIFFRACTION99
2.3379-2.51840.39011320.33552472X-RAY DIFFRACTION100
2.5184-2.77180.30621330.28352532X-RAY DIFFRACTION100
2.7718-3.17280.29641320.2432520X-RAY DIFFRACTION100
3.1728-3.9970.22951340.21262556X-RAY DIFFRACTION100
3.997-46.37030.21291420.20422690X-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)
10.69451.06740.0622.12091.04631.11790.76450.96850.1126-0.3386-0.1829-0.44770.66730.9142-0.00260.97120.07120.24581.2106-0.10220.990335.55535.26186.1958
23.99293.0176-0.76823.83650.76095.62040.1732-1.02520.6020.13950.0358-0.8459-0.71421.33630.07440.7397-0.1540.14470.8826-0.22630.851733.687740.558723.133
32.08481.5121.59591.09671.15021.2301-0.8239-0.4966-0.46610.9354-0.75590.8533-0.067-0.7812-0.76771.45390.73360.66191.2380.1540.885712.215746.832420.2509
42.34221.1102-1.90511.43220.22513.51640.3522-0.6117-0.31550.1263-0.210.24540.87980.5389-0.00260.7113-0.03020.02020.6935-0.05930.648123.655622.815633.4563
52.03713.444-0.98249.2241-1.91010.4649-0.22320.308-0.07370.49460.62942.38340.08060.0086-0.02111.03610.21520.16931.56430.28670.817812.357810.627359.4458
62.51830.662-1.91123.6359-1.59842.0050.0187-0.3192-0.071-0.0220.30420.10270.2403-0.4908-00.5888-0.06190.08010.7043-0.04430.619721.452427.440324.0159
72.05670.56930.38620.82680.69031.8470.45710.3561.2387-1.0022-0.3353-0.7106-0.60010.5320.00060.75690.02120.20950.5446-0.02470.813427.696740.03319.6118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 901 through 914 )
2X-RAY DIFFRACTION2chain 'A' and (resid 915 through 983 )
3X-RAY DIFFRACTION3chain 'A' and (resid 984 through 992 )
4X-RAY DIFFRACTION4chain 'A' and (resid 993 through 1039 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1040 through 1086 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1087 through 1142 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1143 through 1162 )

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