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- PDB-4bpu: Crystal structure of human primase in heterodimeric form, compris... -

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Basic information

Entry
Database: PDB / ID: 4bpu
TitleCrystal structure of human primase in heterodimeric form, comprising PriS and truncated PriL lacking the C-terminal Fe-S domain.
Components
  • DNA PRIMASE LARGE SUBUNIT
  • DNA PRIMASE SMALL SUBUNIT
KeywordsTRANSFERASE / DNA-DEPENDENT RNA POLYMERASE
Function / homology
Function and homology information


DNA primase AEP / ribonucleotide binding / DNA replication initiation / Telomere C-strand synthesis initiation / DNA/RNA hybrid binding / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / Removal of the Flap Intermediate ...DNA primase AEP / ribonucleotide binding / DNA replication initiation / Telomere C-strand synthesis initiation / DNA/RNA hybrid binding / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / DNA replication, synthesis of primer / DNA replication initiation / Activation of the pre-replicative complex / Defective pyroptosis / DNA-directed RNA polymerase activity / 4 iron, 4 sulfur cluster binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / membrane
Similarity search - Function
Transcription Elongation Factor S-II; Chain A - #80 / DNA primase, PRIM domain / DNA primase, PRIM domain / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, large subunit, eukaryotic / DNA primase, small subunit / DNA primase small subunit / DNA primase large subunit, eukaryotic/archaeal / Eukaryotic and archaeal DNA primase, large subunit C-terminal domain / Transcription Elongation Factor S-II; Chain A ...Transcription Elongation Factor S-II; Chain A - #80 / DNA primase, PRIM domain / DNA primase, PRIM domain / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, large subunit, eukaryotic / DNA primase, small subunit / DNA primase small subunit / DNA primase large subunit, eukaryotic/archaeal / Eukaryotic and archaeal DNA primase, large subunit C-terminal domain / Transcription Elongation Factor S-II; Chain A / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA primase small subunit / DNA primase large subunit
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.7 Å
AuthorsKilkenny, M.L. / Perera, R.L. / Pellegrini, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of Human Primase Reveal Design of Nucleotide Elongation Site and Mode of Pol Alpha Tethering
Authors: Kilkenny, M.L. / Longo, M. / Perera, R.L. / Pellegrini, L.
History
DepositionMay 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: DNA PRIMASE SMALL SUBUNIT
B: DNA PRIMASE LARGE SUBUNIT
C: DNA PRIMASE SMALL SUBUNIT
D: DNA PRIMASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,28010
Polymers159,7804
Non-polymers4996
Water3,855214
1
A: DNA PRIMASE SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5426
Polymers50,1081
Non-polymers4345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: DNA PRIMASE SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1732
Polymers50,1081
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: DNA PRIMASE LARGE SUBUNIT


Theoretical massNumber of molelcules
Total (without water)29,7821
Polymers29,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA PRIMASE LARGE SUBUNIT


Theoretical massNumber of molelcules
Total (without water)29,7821
Polymers29,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.550, 68.640, 126.760
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein DNA PRIMASE SMALL SUBUNIT / DNA PRIMASE 49 KDA SUBUNIT / P49


Mass: 50108.023 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: P49642, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein DNA PRIMASE LARGE SUBUNIT / DNA PRIMASE 58 KDA SUBUNIT / P58


Mass: 29782.174 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: P49643, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growDetails: 100MM TRIS-HCL/BICINE PH 8.5, 20% GLYCEROL, 10% PEG4000 AND 20MM EACH OF AN ALCOHOL MIX COMPRISING 1,6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4- BUTANEDIOL AND 1,3-PROPANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9763
DetectorDetector: CCD / Date: Jun 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→29.96 Å / Num. obs: 52124 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 81.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.7→29.617 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 27.74 / Stereochemistry target values: MLHL
Details: THE STRUCTURE WAS REFINED IN PHENIX WITH RIDING HYDROGENS. THE HYDROGENS HAVE BEEN INCLUDED IN THE ENTRY.
RfactorNum. reflection% reflection
Rfree0.2454 2656 5.1 %
Rwork0.2028 --
obs0.2051 52054 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.7 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9768 0 26 214 10008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710092
X-RAY DIFFRACTIONf_angle_d0.95413598
X-RAY DIFFRACTIONf_dihedral_angle_d12.9893849
X-RAY DIFFRACTIONf_chiral_restr0.041458
X-RAY DIFFRACTIONf_plane_restr0.0061731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74910.41021340.33272655X-RAY DIFFRACTION100
2.7491-2.80190.35591320.30712558X-RAY DIFFRACTION99
2.8019-2.85910.31681390.282630X-RAY DIFFRACTION99
2.8591-2.92120.29551280.26632586X-RAY DIFFRACTION99
2.9212-2.98910.32341480.25742630X-RAY DIFFRACTION100
2.9891-3.06370.28651420.26342590X-RAY DIFFRACTION99
3.0637-3.14650.30281420.25342601X-RAY DIFFRACTION100
3.1465-3.2390.33921380.24412621X-RAY DIFFRACTION100
3.239-3.34340.28971380.22922621X-RAY DIFFRACTION99
3.3434-3.46270.28491440.22012611X-RAY DIFFRACTION99
3.4627-3.60110.24971240.21782625X-RAY DIFFRACTION99
3.6011-3.76470.23591430.2092575X-RAY DIFFRACTION100
3.7647-3.96270.26141670.20062623X-RAY DIFFRACTION100
3.9627-4.21040.2431410.18812626X-RAY DIFFRACTION99
4.2104-4.53440.19931390.17032629X-RAY DIFFRACTION99
4.5344-4.98880.22371290.17172639X-RAY DIFFRACTION99
4.9888-5.70620.21421540.18482633X-RAY DIFFRACTION99
5.7062-7.17230.24641390.20442637X-RAY DIFFRACTION99
7.1723-29.61860.21491350.18052308X-RAY DIFFRACTION84

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