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- PDB-4hfx: Crystal structure of a transcription elongation factor B polypept... -

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Basic information

Entry
Database: PDB / ID: 4hfx
TitleCrystal structure of a transcription elongation factor B polypeptide 3 from Homo sapiens, Northeast Structural Genomics consortium target id HR4748B.
ComponentsTranscription elongation factor B polypeptide 3
KeywordsTRANSCRIPTION / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


elongin complex / site of DNA damage / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation ...elongin complex / site of DNA damage / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3180 / RNA polymerase II transcription factor SIII, subunit A / : / RNA polymerase II transcription factor SIII (Elongin) subunit A / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS N-terminal domain profile. / F-box domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3180 / RNA polymerase II transcription factor SIII, subunit A / : / RNA polymerase II transcription factor SIII (Elongin) subunit A / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS N-terminal domain profile. / F-box domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / F-box domain / TFIIS/LEDGF domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.54 Å
AuthorsSeetharaman, J. / Su, M. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a transcription elongation factor B polypeptide 3 from Homo sapiens, Northeast Structural Genomics consortium target id HR4748B. (CASP Target)
Authors: Seetharaman, J. / Su, M. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / K Everett, J. / T Montelione, G. / Hunt, J.F. / Tong, L.
History
DepositionOct 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription elongation factor B polypeptide 3
B: Transcription elongation factor B polypeptide 3
C: Transcription elongation factor B polypeptide 3
D: Transcription elongation factor B polypeptide 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8657
Polymers48,5774
Non-polymers2883
Water72140
1
A: Transcription elongation factor B polypeptide 3
D: Transcription elongation factor B polypeptide 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3843
Polymers24,2882
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-22 kcal/mol
Surface area8240 Å2
MethodPISA
2
B: Transcription elongation factor B polypeptide 3
C: Transcription elongation factor B polypeptide 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4814
Polymers24,2882
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-40 kcal/mol
Surface area8330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.643, 80.643, 63.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.555574, 0.826204, 0.093409), (0.830698, -0.546716, -0.10508), (-0.03575, 0.135974, -0.990067)-5.33186, 0.59902, 34.41256
3given(-0.99994, 0.001111, 0.010909), (-0.001105, -0.999999, 0.000593), (0.01091, 0.000581, 0.99994)40.07086, 23.21929, -0.15835
4given(-0.56932, -0.817277, 0.089069), (-0.821917, 0.563448, -0.083547), (0.018095, -0.120772, -0.992515)36.34018, 20.52642, 35.87799

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Components

#1: Protein
Transcription elongation factor B polypeptide 3 / Elongin 110 kDa subunit / Elongin-A / EloA / RNA polymerase II transcription factor SIII subunit A1 ...Elongin 110 kDa subunit / Elongin-A / EloA / RNA polymerase II transcription factor SIII subunit A1 / SIII p110


Mass: 12144.203 Da / Num. of mol.: 4 / Fragment: F-box domain residues 597-682 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14241
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 277 K / Method: microbatch under oil method / pH: 9
Details: 1.88M Na2s2o3, 0.1M TAPS PH9, Microbatch under oil method, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: May 20, 2012
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.386
11-K, -H, -L20.113
11-h,-k,l30.389
11K, H, -L40.113
ReflectionResolution: 2.54→50 Å / Num. obs: 15239 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.06 / Rsym value: 0.05 / Net I/σ(I): 17.6
Reflection shellResolution: 2.54→2.63 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.377 / Num. unique all: 1257 / Rsym value: 0.348 / % possible all: 81

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.54→28.8 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.89 / SU B: 18.604 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26283 811 5.5 %RANDOM
Rwork0.23476 ---
obs0.23634 14045 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.833 Å2
Baniso -1Baniso -2Baniso -3
1-15.62 Å20 Å20 Å2
2--15.62 Å20 Å2
3----31.25 Å2
Refinement stepCycle: LAST / Resolution: 2.54→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 15 40 1872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191854
X-RAY DIFFRACTIONr_bond_other_d0.0020.021714
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.9842497
X-RAY DIFFRACTIONr_angle_other_deg0.75233884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4475212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78122.376101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51815308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3361528
X-RAY DIFFRACTIONr_chiral_restr0.0530.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02446
LS refinement shellResolution: 2.537→2.603 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 62 -
Rwork0.357 810 -
obs--76.83 %
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)
12.5817-0.0115-0.02421.4177-0.45210.459-0.0882-0.28470.11620.1944-0.0364-0.0240.0369-0.02830.12460.06920.00730.02860.1211-0.01040.057213.757623.209324.6943
23.28772.07-0.4861.6276-0.38051.1052-0.08780.10290.0639-0.1142-0.0882-0.0464-0.03430.06320.17590.1318-0.0025-0.01360.1471-0.00140.101231.61584.110111.0919
35.07261.56641.66680.70380.2371.1954-0.123-0.1542-0.2383-0.0085-0.004-0.1920.11890.00030.1270.15290.05380.0170.09270.01840.093825.22371.047822.707
45.21163.1563-1.20671.9196-0.73110.3003-0.10870.1197-0.0665-0.06520.036-0.03420.0304-0.00530.07270.1336-0.00830.03280.17810.030.17387.940917.809912.0402
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 81
2X-RAY DIFFRACTION2B8 - 81
3X-RAY DIFFRACTION3C8 - 81
4X-RAY DIFFRACTION4D7 - 78

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