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- PDB-4zn1: Crystal Structure of MjSpt4:Spt5 complex conformation A -

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Basic information

Entry
Database: PDB / ID: 4zn1
TitleCrystal Structure of MjSpt4:Spt5 complex conformation A
Components
  • Transcription elongation factor Spt4
  • Transcription elongation factor Spt5
KeywordsTRANSCRIPTION / protein-protein complex
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / translation elongation factor activity / regulation of DNA-templated transcription elongation / structural constituent of ribosome / ribosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / zinc ion binding
Similarity search - Function
Rubrerythrin, domain 2 - #90 / Archaeal transcription elongation factor Spt4 / Transcription elongation factor Spt5, archaeal / Archaeal transcription elongation factor Spt4 superfamily / NusG, N-terminal domain / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / NGN domain / Transcription elongation factor SPT5 ...Rubrerythrin, domain 2 - #90 / Archaeal transcription elongation factor Spt4 / Transcription elongation factor Spt5, archaeal / Archaeal transcription elongation factor Spt4 superfamily / NusG, N-terminal domain / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / SH3 type barrels. - #30 / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / Rubrerythrin, domain 2 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Single Sheet / SH3 type barrels. / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Roll / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transcription elongation factor Spt5 / Transcription elongation factor Spt4
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGuo, G.R. / Zhou, H.H. / Gao, Y.X. / Zhu, Z.L. / Niu, L.W. / Teng, M.K.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural and biochemical insights into the DNA-binding mode of MjSpt4p:Spt5 complex at the exit tunnel of RNAPII
Authors: Guo, G.R. / Gao, Y.X. / Zhu, Z.L. / Zhao, D. / Liu, Z. / Zhou, H.H. / Niu, L.W. / Teng, M.K.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription elongation factor Spt5
B: Transcription elongation factor Spt4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3003
Polymers24,2342
Non-polymers651
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-13 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.820, 84.820, 34.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein Transcription elongation factor Spt5


Mass: 16158.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: spt5 / Plasmid: pRSFDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57818
#2: Protein Transcription elongation factor Spt4


Mass: 8075.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: spt4 / Plasmid: pRSFDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57839
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 5000MME, propanol, MES, sarcosine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→37.93 Å / Num. obs: 6086 / % possible obs: 99.6 % / Redundancy: 4 % / Net I/σ(I): 20.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EWG, 1RYQ, 1NPP

3ewg

1ryq

1npp


Resolution: 2.8→37.93 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.904 / SU B: 15.284 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 1.525 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28247 290 4.7 %RANDOM
Rwork0.24222 ---
obs0.24392 5929 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.501 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20 Å2
2---1.24 Å20 Å2
3---2.47 Å2
Refinement stepCycle: LAST / Resolution: 2.8→37.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 1 16 1406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191405
X-RAY DIFFRACTIONr_bond_other_d0.0020.021335
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9921911
X-RAY DIFFRACTIONr_angle_other_deg0.97533069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.61326.81844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.08615218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.51153
X-RAY DIFFRACTIONr_chiral_restr0.0740.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211578
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02247
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2477.355783
X-RAY DIFFRACTIONr_mcbond_other3.2477.357782
X-RAY DIFFRACTIONr_mcangle_it5.24411.018970
X-RAY DIFFRACTIONr_mcangle_other5.24211.016971
X-RAY DIFFRACTIONr_scbond_it3.2637.584622
X-RAY DIFFRACTIONr_scbond_other3.2557.588620
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.36311.28941
X-RAY DIFFRACTIONr_long_range_B_refined8.07157.0021419
X-RAY DIFFRACTIONr_long_range_B_other8.06857.0061420
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 21 -
Rwork0.379 449 -
obs--99.79 %

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