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- PDB-3qqc: Crystal structure of archaeal Spt4/5 bound to the RNAP clamp domain -

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Basic information

Entry
Database: PDB / ID: 3qqc
TitleCrystal structure of archaeal Spt4/5 bound to the RNAP clamp domain
Components
  • DNA-directed RNA polymerase subunit b, DNA-directed RNA polymerase subunit a', DNA-directed RNA polymerase subunit A''
  • DNA-directed RNA polymerase, subunit e''
  • Transcription antitermination protein nusG
KeywordsTRANSCRIPTION / fusion protein / chimera protein / multiprotein complex
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / translation elongation factor activity / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / structural constituent of ribosome / ribosome / mRNA binding ...transcription elongation-coupled chromatin remodeling / translation elongation factor activity / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / structural constituent of ribosome / ribosome / mRNA binding / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
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 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger ...Rubrerythrin, domain 2 - #90 / Archaeal transcription elongation factor Spt4 / Transcription elongation factor Spt5, archaeal / Archaeal transcription elongation factor Spt4 superfamily / NusG, N-terminal domain / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / 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 / 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 Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Single Sheet / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transcription elongation factor Spt5 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / Transcription elongation factor Spt4
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular Replacement with SAD / Resolution: 3.3 Å
AuthorsMartinez-Rucobo, F.W.
CitationJournal: Embo J. / Year: 2011
Title: Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity.
Authors: Martinez-Rucobo, F.W. / Sainsbury, S. / Cheung, A.C. / Cramer, P.
History
DepositionFeb 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Aug 9, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.4Sep 13, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Chain A is a fusion protein of three peptides. First peptide is DNA-directed RNA polymerase subunit ...Chain A is a fusion protein of three peptides. First peptide is DNA-directed RNA polymerase subunit b (residues 2-64 in this entry corresponding to UNP Q8U0M3 residues 1053-1115) which is linked (via two GLY GLY linker residues) to DNA-directed RNA polymerase subunit a' (residues 67-382 in this entry corresponding to UNP Q8U0M4 residues 3-318) which is then linked (via nine linker residues: GLY ALA GLY SER GLY ALA GLY SER GLY) to DNA-directed RNA polymerase subunit A'' (residues 392-429 in this entry corresponding to UNP Q8U0M5 residues 334-371).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit b, DNA-directed RNA polymerase subunit a', DNA-directed RNA polymerase subunit A''
D: Transcription antitermination protein nusG
E: DNA-directed RNA polymerase, subunit e''
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7387
Polymers74,4763
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-22 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.570, 107.040, 51.090
Angle α, β, γ (deg.)90.00, 97.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA-directed RNA polymerase subunit b, DNA-directed RNA polymerase subunit a', DNA-directed RNA polymerase subunit A''


Mass: 49409.867 Da / Num. of mol.: 1
Fragment: DNA-directed RNA polymerase subunit B (residues 1053-1115), DNA-directed RNA polymerase subunit A' (residues 3-318), DNA-directed RNA polymerase subunit A'' (residues 334-371)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1563 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8U0M3, UniProt: Q8U0M4, UniProt: Q8U0M5
#2: Protein Transcription antitermination protein nusG


Mass: 18100.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1990 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZK1
#3: Protein DNA-directed RNA polymerase, subunit e''


Mass: 6965.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF0255 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U440
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10% PEG 8000, 0.1 M sodium/potassium phosphate, 0.15 M guanidinium hydrochloride, 0.2 M sodium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.2783 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2783 Å / Relative weight: 1
ReflectionResolution: 3.3→50.7 Å / Num. all: 13603 / Num. obs: 13603 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 92.3 Å2 / Rsym value: 0.14 / Net I/σ(I): 7.4
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1965 / Rsym value: 0.84 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: Molecular Replacement with SAD
Starting model: PDB Entry 1Y1W

1y1w


Resolution: 3.3→50.7 Å / Cor.coef. Fo:Fc: 0.9259 / Cor.coef. Fo:Fc free: 0.893 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The model was subdivided into five groups for TLS refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 674 4.96 %RANDOM
Rwork0.193 ---
all0.195 13601 --
obs0.195 13601 99.8 %-
Displacement parametersBiso mean: 131.01 Å2
Baniso -1Baniso -2Baniso -3
1--13.1219 Å20 Å2-1.1948 Å2
2--1.0587 Å20 Å2
3---12.0632 Å2
Refine analyzeLuzzati coordinate error obs: 0.82 Å
Refinement stepCycle: LAST / Resolution: 3.3→50.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4183 0 4 0 4187
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0142612
X-RAY DIFFRACTIONt_angle_deg1.3757442
X-RAY DIFFRACTIONt_dihedral_angle_d15462
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1042
X-RAY DIFFRACTIONt_gen_planes6005
X-RAY DIFFRACTIONt_it426120
X-RAY DIFFRACTIONt_nbd05
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion24.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion5605
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance151
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact50134
LS refinement shellResolution: 3.3→3.56 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.292 136 4.89 %
Rwork0.216 2646 -
all0.2191 2782 -
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)
15.584-0.83870.72052.581-0.12523.34250.37440.3199-0.6703-0.23390.04870.2841-0.0158-0.2399-0.4231-0.07710.1780.0383-0.03440.0157-0.3312-24.695819.7-10.8523
24.7701-1.3331-3.341.7285-2.3183.14360.0076-1.18780.13290.50960.1787-0.1134-0.7229-0.2644-0.18630.10350.08610.08160.2285-0.0023-0.3243-17.580425.256410.7407
314.96160.6583-0.50910.1844-3.5897-0.35890.15880.5253-0.5918-0.17610.24420.343-0.38160.1625-0.4030.11430.2262-0.08310.09960.042-0.3121-6.325323.4059-2.9949
410.9571.67591.449312.5932-0.101913.03260.01771.38530.5284-1.110.24791.5071-0.381-0.2734-0.2656-0.5510.0494-0.3398-0.01960.37610.3044-51.163728.7204-29.839
55.03871.81622.442613.33640.41080.56730.1201-0.08610.01150.15430.03711.1890.484-0.8067-0.1573-0.67110.1304-0.1740.46790.21710.5797-67.986629.838-24.3479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|67 - 371 }A67 - 371
2X-RAY DIFFRACTION2{ A|2 - 64 }A2 - 64
3X-RAY DIFFRACTION3{ A|407 - 436 }A407 - 436
4X-RAY DIFFRACTION4{ D|* }D4 - 85
5X-RAY DIFFRACTION5{ E|* }E3 - 60

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