PDB-6rb4: Crystal structure of the Pri1 subunit of human primase

ID or keywords:

Entry

Database: PDB / ID: 6rb4

Title

Crystal structure of the Pri1 subunit of human primase

Components

DNA primase small subunit

Primase

Keywords

REPLICATION /

Primase /

DNA-dependent RNA polymerase /

ATP / priming

Function / homology

Function and homology information

DNA primase AEP /

ribonucleotide binding / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / Removal of the Flap Intermediate /

DNA primase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Kilkenny, M.L. / Pellegrini, L.

Funding support

United Kingdom, 1items

Citation

Journal: Acs Chem.Biol. / Year: 2019
Title: Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine.
Authors: Holzer, S. / Rzechorzek, N.J. / Short, I.R. / Jenkyn-Bedford, M. / Pellegrini, L. / Kilkenny, M.L.

History

Deposition	Apr 9, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 11, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 2, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6rb4.cif.gz	181.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6rb4.ent.gz	143.6 KB	Display	PDB format
PDBx/mmJSON format	6rb4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rb/6rb4 ftp://data.pdbj.org/pub/pdb/validation_reports/rb/6rb4	HTTPS FTP

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Related structure data

Related structure data	6r4sC 6r4tC 6r4uC 6r5dC 6r5eC 4bpuS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6r4s-1 6r5e-2 6r4t-2 5jd3-9 4jko-d 6r4s-2 4xpu-d 6orf-1 4i2y-1 5jd3-12 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#150 - Jun 2012 Sliding Clamps similarity (4) #47 - Nov 2003 Simian Virus 40 similarity (1) #236 - Aug 2019 Cyclin and Cyclin-dependent Kinase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: DNA primase small subunit

hetero molecules

49 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	78.659, 78.659, 148.335
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	DNA primase small subunit / Primase / DNA primase 49 kDa subunit / p49 Mass: 48720.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 References: UniProt: P49642, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#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 / Water Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.76 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 100mM Bis Tris propane pH 6.5, 24 % PEG 3350, 150 mM NaF

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98011 Å / Relative weight: 1
Reflection	Resolution: 1.5→44.5 Å / Num. obs: 75113 / % possible obs: 99.89 % / Redundancy: 2 % / CC_1/2: 1 / R_rim(I) all: 0.02722 / Net I/σ(I): 15.76
Reflection shell	Resolution: 1.5→1.554 Å / Redundancy: 2 % / R_merge(I) obs: 0.5433 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 7355 / CC_1/2: 0.655 / % possible all: 99.35

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
Coot		model building
PHENIX		refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4BPU

4bpu

Resolution: 1.5→44.498 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.96

	R_factor	Num. reflection	% reflection
R_free	0.2148	3785	5.04 %
R_work	0.1929	-	-
obs	0.1941	75090	99.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.5→44.498 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3260	0	17	465	3742

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3485
X-RAY DIFFRACTION	f_angle_d	0.844	4717
X-RAY DIFFRACTION	f_dihedral_angle_d	12.962	2111
X-RAY DIFFRACTION	f_chiral_restr	0.055	492
X-RAY DIFFRACTION	f_plane_restr	0.007	608

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.5-1.519	0.4178	152	0.3717	2558	X-RAY DIFFRACTION	98
1.519-1.539	0.3724	131	0.3648	2592	X-RAY DIFFRACTION	100
1.539-1.5601	0.3959	120	0.3285	2604	X-RAY DIFFRACTION	100
1.5601-1.5824	0.3262	118	0.3126	2617	X-RAY DIFFRACTION	100
1.5824-1.606	0.2942	151	0.2884	2606	X-RAY DIFFRACTION	100
1.606-1.6311	0.3526	143	0.2841	2598	X-RAY DIFFRACTION	100
1.6311-1.6578	0.2749	137	0.2721	2596	X-RAY DIFFRACTION	100
1.6578-1.6864	0.2805	134	0.2711	2624	X-RAY DIFFRACTION	100
1.6864-1.7171	0.3211	135	0.259	2611	X-RAY DIFFRACTION	100
1.7171-1.7501	0.2851	155	0.2594	2611	X-RAY DIFFRACTION	100
1.7501-1.7858	0.2488	123	0.2467	2623	X-RAY DIFFRACTION	100
1.7858-1.8246	0.2975	143	0.2384	2603	X-RAY DIFFRACTION	100
1.8246-1.8671	0.2534	139	0.2452	2632	X-RAY DIFFRACTION	100
1.8671-1.9138	0.2979	137	0.2333	2620	X-RAY DIFFRACTION	100
1.9138-1.9655	0.2597	150	0.2326	2612	X-RAY DIFFRACTION	100
1.9655-2.0234	0.2567	136	0.2151	2624	X-RAY DIFFRACTION	100
2.0234-2.0887	0.236	135	0.2015	2622	X-RAY DIFFRACTION	100
2.0887-2.1633	0.2383	138	0.199	2642	X-RAY DIFFRACTION	100
2.1633-2.2499	0.2457	127	0.1972	2658	X-RAY DIFFRACTION	100
2.2499-2.3523	0.2047	143	0.1838	2629	X-RAY DIFFRACTION	100
2.3523-2.4763	0.2003	139	0.1834	2679	X-RAY DIFFRACTION	100
2.4763-2.6315	0.2047	166	0.1772	2617	X-RAY DIFFRACTION	100
2.6315-2.8346	0.217	143	0.1769	2669	X-RAY DIFFRACTION	100
2.8346-3.1198	0.2029	144	0.1745	2686	X-RAY DIFFRACTION	100
3.1198-3.5711	0.1983	152	0.1673	2718	X-RAY DIFFRACTION	100
3.5711-4.4985	0.1615	145	0.1445	2740	X-RAY DIFFRACTION	100
4.4985-44.5175	0.1575	149	0.1781	2914	X-RAY DIFFRACTION	100

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