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- PDB-6k7p: Crystal structure of human AFF4-THD domain -

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Basic information

Entry
Database: PDB / ID: 6k7p
TitleCrystal structure of human AFF4-THD domain
ComponentsAF4/FMR2 family member 4
KeywordsTRANSCRIPTION / Super Elongation Complex / AFF4 / HIV-1 / dimerizaiton
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 / SAD / Resolution: 2.4 Å
AuthorsTang, D. / Xue, Y. / Li, S. / Cheng, W. / Duan, J. / Wang, J. / Qi, S.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2018YFC1004601 China
Ministry of Science and Technology (China)2017YFA0506300 China
National Science Foundation (China)81671388 China
CitationJournal: Cell Discov / Year: 2020
Title: Structural and functional insight into the effect of AFF4 dimerization on activation of HIV-1 proviral transcription.
Authors: Tang, D. / Chen, C. / Liao, G. / Liu, J. / Liao, B. / Huang, Q. / Chen, Q. / Zhao, J. / Jiang, H. / Duan, J. / Huang, J. / Wang, K. / Wang, J. / Zhou, C. / Chu, W. / Li, W. / Sun, B. / Li, Z. ...Authors: Tang, D. / Chen, C. / Liao, G. / Liu, J. / Liao, B. / Huang, Q. / Chen, Q. / Zhao, J. / Jiang, H. / Duan, J. / Huang, J. / Wang, K. / Wang, J. / Zhou, C. / Chu, W. / Li, W. / Sun, B. / Li, Z. / Dai, L. / Fu, X. / Cheng, W. / Xue, Y. / Qi, S.
History
DepositionJun 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Refinement description / Category: citation / pdbx_refine_tls_group
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AF4/FMR2 family member 4


Theoretical massNumber of molelcules
Total (without water)30,4701
Polymers30,4701
Non-polymers00
Water21612
1
A: AF4/FMR2 family member 4

A: AF4/FMR2 family member 4


Theoretical massNumber of molelcules
Total (without water)60,9392
Polymers60,9392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area3040 Å2
ΔGint-25 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.411, 79.762, 185.667
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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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: 30469.623 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.: 12 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 4.5
Details: 0.3 M sodium citrate, 0.1 M sodium citrate-citrate acid pH 4.5, 25% PEG 3350
PH range: 4-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 25, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.399→50 Å / Num. obs: 12455 / % possible obs: 99.6 % / Redundancy: 19 % / Biso Wilson estimate: 55.81 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.02 / Rrim(I) all: 0.087 / Χ2: 0.72 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4915.90.53511720.9750.1330.5510.47696.2
2.49-2.5918.30.46112410.990.1090.4740.599.4
2.59-2.720.10.38611950.9910.0880.3960.528100
2.7-2.85200.26812280.9940.0610.2750.579100
2.85-3.0219.90.18112500.9960.0410.1860.708100
3.02-3.2618.30.13712230.9970.0330.1410.87100
3.26-3.5820.20.10212600.9980.0230.1040.967100
3.58-4.1200.07812660.9980.0180.080.89100
4.1-5.1718.40.06612740.9990.0160.0680.733100
5.17-5018.30.06513460.9980.0160.0670.86699.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.4→46.417 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 33.24
RfactorNum. reflection% reflection
Rfree0.2676 1246 10.02 %
Rwork0.2137 --
obs0.2191 12440 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.01 Å2 / Biso mean: 75.6896 Å2 / Biso min: 35.69 Å2
Refinement stepCycle: final / Resolution: 2.4→46.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 0 12 1769
Biso mean---60.85 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091792
X-RAY DIFFRACTIONf_angle_d1.0432418
X-RAY DIFFRACTIONf_chiral_restr0.05269
X-RAY DIFFRACTIONf_plane_restr0.006305
X-RAY DIFFRACTIONf_dihedral_angle_d9.9711095
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.4950.43591300.2934116295
2.495-2.60850.33461340.2585121399
2.6085-2.7460.30041380.23131232100
2.746-2.9180.32331360.2411223100
2.918-3.14330.32651380.22841243100
3.1433-3.45950.281400.22341253100
3.4595-3.95990.23741390.2131247100
3.9599-4.98810.23491410.181275100
4.9881-46.4170.25691500.2141346100
Refinement TLS params.Method: refined / Origin x: 5.5286 Å / Origin y: 8.2177 Å / Origin z: 67.7266 Å
111213212223313233
T0.3961 Å2-0.0332 Å2-0.071 Å2-0.4197 Å2-0.0558 Å2--0.4313 Å2
L1.1069 °2-0.6337 °21.492 °2-1.8896 °2-1.4861 °2--3.2641 °2
S0.2076 Å °0.2578 Å °-0.26 Å °0.0132 Å °-0.0183 Å °-0.094 Å °0.0362 Å °0.5583 Å °0.2916 Å °
Refinement TLS groupSelection details: all

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