4BPU: DNA primase small subunit

Crystal structure of human primase in heterodimeric form, comprising PriS and truncated PriL lacking the C-terminal Fe-S domain. Determined by X-ray diffraction at 2.7 Å resolution. Released 25 Sept 2013.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 10,074
Mol. weight: 160.28 kDa
Ligands: ZN
Released: 25 Sept 2013

Explore 4BPU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4BPU contains 73 α-helices and 34 β-strands across 4 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: 24 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	43-49	7	1
α-helix	50-52	3
β-strand	53-58	6	1
α-helix	63-73	11
β-strand	77-84	8	1
α-helix	88-93	6
β-strand	101-103	3	1
β-strand	106-111	6	2
α-helix	112-115	4
α-helix	129-144	16
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	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	265-281	17
α-helix	292-301	10
α-helix	307-311	5
β-strand	317-318	2	1
β-strand	323	1	3
β-strand	329	1	4
β-strand	330	1	3
β-strand	333	1	2
α-helix	336-341	6
α-helix	348	1
β-strand	349	1	4
α-helix	350-357	8
α-helix	383-385	3
α-helix	389-407	19

Chain B: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	32-33	2
α-helix	39-61	23
α-helix	68-80	13
α-helix	96-109	14
α-helix	114-133	20
α-helix	137-145	9
β-strand	152-153	2	5
α-helix	156-159	4
α-helix	163-169	7
β-strand	183-187	5	5
α-helix	188-191	4
α-helix	192-195	4
β-strand	201-203	3	5
β-strand	206-210	5	5
α-helix	211-235	25
α-helix	244-246	3

Chain C: 24 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	43-49	7	6
α-helix	50-52	3
β-strand	53-58	6	6
α-helix	63-73	11
β-strand	77-84	8	6
α-helix	88-93	6
α-helix	95	1
β-strand	101-103	3	6
β-strand	106-111	6	7
α-helix	112-115	4
α-helix	133-144	12
α-helix	145-149	5
β-strand	155-159	5	7
β-strand	164-169	6	7
α-helix	172-175	4
α-helix	179-189	11
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	292-301	10
α-helix	307-311	5
β-strand	317-318	2	6
β-strand	323	1	8
β-strand	329	1	9
β-strand	330	1	8
β-strand	333	1	7
α-helix	336-341	6
α-helix	348	1
β-strand	349	1	9
α-helix	350-356	7
α-helix	389-407	19

Chain D: 13 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	32-33	2
α-helix	39-62	24
α-helix	68-80	13
α-helix	95-110	16
α-helix	114-133	20
α-helix	137-145	9
β-strand	152-153	2	10
α-helix	156-159	4
α-helix	163-169	7
β-strand	184-187	4	10
α-helix	188-191	4
α-helix	192-195	4
β-strand	201-203	3	10
β-strand	206-209	4	10
α-helix	211-236	26
α-helix	244-246	3
α-helix	247-251	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA primase small subunit	A, C	protein	423	HOMO SAPIENS	P49642 (AlphaFold model)
DNA primase large subunit	B, D	protein	253	HOMO SAPIENS	P49643 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4BPU_1 DNA PRIMASE SMALL SUBUNIT (chains A, C)
GTSMETFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRY
QSFNNQSDLEKEMQAANPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDD
VRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKL
SSAVRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENK
ESWDKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIM
LQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICREL
DAISTNEEEKEENEAESDVKHRTRDYKKTSLAPYVKVFEHFLENLDKSRKGELLKKSDLQ
KDF

Sequence of entity 2 (B, D), FASTA

>4BPU_2 DNA PRIMASE LARGE SUBUNIT (chains B, D)
MEFSGRKWRKLRLAGDQRNASYPHCLQFYLQPPSENISLIEFENLAIDRVKLLKSVENLG
VSYVKGTEQYQSKLESELRKLKFSYRENLEDEYEPRRRDHISHFILRLAYCQSEELRRWF
IQQEMDLLRFRFSILPKDKIQDFLKDSQLQFEAISDEEKTLREQEIVASSPSLSGLKLGF
ESIYKIPFADALDLFRGRKVYLEDGFAYVPLKDIVAIILNEFRAKLSKALALTARSLPAV
QSDERLQPLLNHL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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

Primary citation

Structures of Human Primase Reveal Design of Nucleotide Elongation Site and Mode of Pol Alpha Tethering. Kilkenny, M.L., Longo, M., Perera, R.L. et al. Proc Natl Acad Sci U S A (2013) 110:15961. DOI 10.1073/PNAS.1311185110 · 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
6R4T 2.35 Å, Crystal structure of the Pri1 subunit of human primase bound to vidarabine 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
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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