6R4T: Pri1 subunit of human primase

Crystal structure of the Pri1 subunit of human primase bound to vidarabine triphosphate. Determined by X-ray diffraction at 2.35 Å resolution. Released 11 Sept 2019.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,632
Mol. weight: 98.82 kDa
Ligands: ZN, MN, HEJ
Released: 11 Sept 2019

Explore 6R4T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6R4T contains 56 α-helices and 26 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 28 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-19	11
α-helix	23-31	9
α-helix	32-34	3
β-strand	43-48	6	1
α-helix	50-52	3
β-strand	54-58	5	1
α-helix	63-73	11
β-strand	77-84	8	1
α-helix	88-90	3
α-helix	95	1
β-strand	101-103	3	1
β-strand	106-111	6	2
α-helix	112-118	7
α-helix	133-144	12
α-helix	145-149	5
β-strand	155-159	5	2
β-strand	164-169	6	2
α-helix	172-175	4
α-helix	179-189	11
α-helix	208-209	2
α-helix	210-223	14
α-helix	224-230	7
α-helix	237-244	8
α-helix	249-251	3
α-helix	252-261	10
α-helix	265-278	14
α-helix	291-301	11
α-helix	307-311	5
β-strand	317-318	2	1
α-helix	319	1
β-strand	323	1	3
β-strand	329	1	4
β-strand	330	1	3
β-strand	333	1	2
α-helix	336-338	3
α-helix	344-346	3
α-helix	348	1
β-strand	349	1	4
α-helix	350-358	9
α-helix	383-385	3
α-helix	389-406	18

Chain D: 28 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	9-19	11
α-helix	23-31	9
α-helix	32-34	3
β-strand	43-48	6	5
α-helix	50-52	3
β-strand	54-58	5	5
α-helix	63-73	11
β-strand	77-84	8	5
α-helix	88-90	3
α-helix	95	1
β-strand	101-103	3	5
β-strand	106-111	6	6
α-helix	112-118	7
α-helix	129-144	16
α-helix	145-149	5
β-strand	155-159	5	6
β-strand	164-169	6	6
α-helix	179-189	11
α-helix	208-209	2
α-helix	210-223	14
α-helix	224-230	7
α-helix	237-244	8
α-helix	249-251	3
α-helix	252-261	10
α-helix	265-278	14
α-helix	291-301	11
α-helix	307-311	5
β-strand	317-318	2	5
α-helix	319	1
β-strand	323	1	7
β-strand	329	1	8
β-strand	330	1	7
β-strand	333	1	6
α-helix	336-338	3
α-helix	344-346	3
α-helix	348	1
β-strand	349	1	8
α-helix	350-357	8
α-helix	383-385	3
α-helix	389-404	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA primase small subunit	A, D	protein	410	Homo sapiens	P49642 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6R4T_1 DNA primase small subunit (chains A, D)
GTSMETFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRY
QSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDD
VRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKL
SSAVRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENK
ESWDKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIM
LQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICREL
DAISTNEEEKEENEAESDVKHRTRDYKKTSLAPYVKVFEHFLENLDKSRK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MN	Manganese (II) ion	Mn	2
HEJ	9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D…	C10 H16 N5 O13 P3	2

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine. Holzer, S., Rzechorzek, N.J., Short, I.R. et al. ACS Chem Biol (2019) 14:1904-1912. DOI 10.1021/acschembio.9b00367 · PubMed

Other PDB entries of the same protein (UniProt P49642 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RB4 1.5 Å, Crystal structure of the Pri1 subunit of human primase
4LIK 1.7 Å, Crystal structure of the catalytic subunit of human primase
6R5E 1.85 Å, Crystal structure of the Pri1 subunit of human primase bound to 2F-ATP
6R5D 1.95 Å, Crystal structure of the Pri1 subunit of human primase bound to dATP
4MHQ 2.2 Å, Crystal structure of human primase catalytic subunit
6R4U 2.2 Å, Crystal structure of the Pri1 subunit of human primase bound to fludarabine triphosphate
4LIL 2.6 Å, Crystal structure of the catalytic subunit of human primase bound to UTP and Mn
4RR2 2.65 Å, Crystal structure of human primase
4BPU 2.7 Å, Crystal structure of human primase in heterodimeric form, comprising PriS and truncated…
6R4S 2.75 Å, Crystal structure of the Pri1 subunit of human primase bound to ATP
8VY3 2.98 Å, Human DNA polymerase alpha/primase - AavLEA1 (1:40 molar ratio)
4BPW 3.0 Å, Crystal structure of human primase bound to UTP

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