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- PDB-5l3x: Crystal structure of negative elongation factor subcomplex NELF-AC -

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Basic information

Entry
Database: PDB / ID: 5l3x
TitleCrystal structure of negative elongation factor subcomplex NELF-AC
Components
  • Negative elongation factor A
  • Negative elongation factor C/D
KeywordsTRANSCRIPTION / repressor / transcription regulation / gene expression
Function / homology
Function and homology information


NELF complex / positive regulation of protein modification process / Abortive elongation of HIV-1 transcript in the absence of Tat / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / negative regulation of transcription elongation by RNA polymerase II / 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 ...NELF complex / positive regulation of protein modification process / Abortive elongation of HIV-1 transcript in the absence of Tat / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / negative regulation of transcription elongation by RNA polymerase II / 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 / TP53 Regulates Transcription of DNA Repair Genes / molecular adaptor activity / nuclear body / chromatin binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
TH1 protein / TH1 protein / Hepatitis delta antigen (HDAg) domain / Hepatitis delta antigen (HDAg) domain profile.
Similarity search - Domain/homology
Negative elongation factor C/D / Negative elongation factor A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.75 Å
AuthorsPoellmann, D. / Vos, S.M. / Cramer, P.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationSFB 860 Germany
European Research CouncilTRANSIT Germany
Volkswagen Foundation Germany
CitationJournal: Elife / Year: 2016
Title: Architecture and RNA binding of the human negative elongation factor.
Authors: Vos, S.M. / Pollmann, D. / Caizzi, L. / Hofmann, K.B. / Rombaut, P. / Zimniak, T. / Herzog, F. / Cramer, P.
History
DepositionMay 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Data collection
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.name
Revision 1.3May 8, 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

Downloads & links

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Assembly

Deposited unit
A: Negative elongation factor A
B: Negative elongation factor C/D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0444
Polymers64,9732
Non-polymers712
Water23413
1
A: Negative elongation factor A
B: Negative elongation factor C/D
hetero molecules

A: Negative elongation factor A
B: Negative elongation factor C/D
hetero molecules

A: Negative elongation factor A
B: Negative elongation factor C/D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,13212
Polymers194,9196
Non-polymers2136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area28260 Å2
ΔGint-265 kcal/mol
Surface area81490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.070, 185.070, 185.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Negative elongation factor A / NELF-A / Wolf-Hirschhorn syndrome candidate 2 protein


Mass: 19479.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NELFA, WHSC2, P/OKcl.15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q9H3P2
#2: Protein Negative elongation factor C/D / NELF-C/D / TH1-like protein


Mass: 45493.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NELFCD, NELFD, TH1, TH1L, HSPC130 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q8IXH7
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.07 Å3/Da / Density % sol: 69.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 14-14.5% (w/v) PEG 3350 200mM sodium malonate pH 6.8-7.0
PH range: 6.8-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 29, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→46.267 Å / Num. obs: 27492 / % possible obs: 100 % / Redundancy: 39.8 % / CC1/2: 1 / Rsym value: 0.09 / Net I/σ(I): 32.2
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 40.7 % / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SHELXDEphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.75→46.267 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.15
RfactorNum. reflection% reflection
Rfree0.2558 1374 5 %
Rwork0.2369 --
obs0.2378 27492 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 216.69 Å2 / Biso mean: 109.036 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.75→46.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4436 0 2 13 4451
Biso mean--103.46 77.4 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034514
X-RAY DIFFRACTIONf_angle_d0.6626122
X-RAY DIFFRACTIONf_chiral_restr0.024728
X-RAY DIFFRACTIONf_plane_restr0.004775
X-RAY DIFFRACTIONf_dihedral_angle_d10.981679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7503-2.84860.43391370.406126072744
2.8486-2.96260.38171340.323425612695
2.9626-3.09740.31311370.296725992736
3.0974-3.26070.31691370.279225982735
3.2607-3.46490.32321360.270925792715
3.4649-3.73240.28441370.258526052742
3.7324-4.10780.26461380.234326242762
4.1078-4.70170.21371370.208226122749
4.7017-5.92160.21181390.220126282767
5.9216-46.2740.2421420.216727052847
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)
12.6772-0.3266-3.33780.02850.33484.74691.2457-0.61192.4616-0.3604-0.4052-0.2003-1.79081.78060.30261.95770.1651-0.61990.67390.16321.562539.874729.127370.8129
22.5025-0.9061-1.08331.2610.34431.15980.06220.40980.9377-0.7436-0.1763-0.8408-0.88340.54930.01311.3455-0.0059-0.21520.7830.29161.028841.185220.631261.2426
32.8279-1.77220.92652.88090.69281.9538-0.50820.3723-1.1999-1.7455-0.0641-0.29510.2377-0.1857-0.02441.18610.1386-0.30890.80430.11560.845927.81046.00757.6602
41.9972-9.3123-7.42348.42948.59692.0071-0.49470.8467-3.3840.4445-1.37791.28272.2442-0.9277-2.2991.19670.0839-0.26321.29890.1821.59816.33416.323658.313
50.4158-0.90640.30941.9751-0.82371.4521-0.3580.0180.18930.52750.36180.28040.0876-0.4415-0.00050.90380.1422-0.02710.5680.10790.873-5.172112.190655.6329
60.05980.11670.01590.0995-0.02540.0938-1.32280.5387-1.48460.6364-0.25050.7094-0.2608-1.45280.00161.47150.39250.11171.15450.13771.2646-22.496127.096862.2751
77.2249-0.8981.55773.2736-2.56742.7816-0.3239-0.36810.32520.31530.44330.1487-0.5358-0.2985-0.00111.01910.2517-0.2920.7237-0.03820.638419.753714.918365.0931
83.8769-0.4713-2.56366.67190.10675.8160.4615-0.14860.74160.78280.2327-0.4255-1.0330.4210.00950.94820.0429-0.1470.46960.04920.913.805331.339851.5599
92.15570.2597-0.14921.8107-0.96241.9326-0.1612-0.71390.03741.33730.01780.7091-0.3707-0.0892-0.00451.5370.18550.31520.81790.10820.9481-11.738313.850474.4631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 29 )A6 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 91 )A30 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 125 )A92 - 125
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 133 )A126 - 133
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 164 )A134 - 164
6X-RAY DIFFRACTION6chain 'A' and (resid 165 through 177 )A165 - 177
7X-RAY DIFFRACTION7chain 'B' and (resid 186 through 302 )B186 - 302
8X-RAY DIFFRACTION8chain 'B' and (resid 303 through 436 )B303 - 436
9X-RAY DIFFRACTION9chain 'B' and (resid 437 through 590 )B437 - 590

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