4BPX: Human primase

Crystal structure of human primase in complex with the primase- binding motif of DNA polymerase alpha. Determined by X-ray diffraction at 3.4 Å resolution. Released 25 Sept 2013.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 9,589
Mol. weight: 161.89 kDa
Ligands: ZN
Released: 25 Sept 2013

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

Secondary structure: helices and β-sheets

4BPX contains 81 α-helices and 35 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: 27 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	112-115	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	174-176	3
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	265-281	17
α-helix	292-301	10
α-helix	303-304	2
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	336-338	3
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	39-58	20
α-helix	73-80	8
α-helix	98-109	12
α-helix	114-133	20
α-helix	137-146	10
β-strand	153	1	5
α-helix	157-161	5
α-helix	163-167	5
β-strand	184-187	4	5
α-helix	188-191	4
α-helix	192-195	4
β-strand	201-203	3	5
β-strand	206-209	4	5
α-helix	213-236	24
α-helix	244-246	3
α-helix	247-252	6

Chain C: 26 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	6
α-helix	50-52	3
β-strand	54-58	5	6
α-helix	63-73	11
β-strand	77-84	8	6
α-helix	88-90	3
α-helix	95	1
β-strand	101-103	3	6
β-strand	106-111	6	7
α-helix	112-115	4
α-helix	133-148	16
β-strand	155-159	5	7
β-strand	164-169	6	7
α-helix	172-175	4
α-helix	179-189	11
α-helix	208-209	2
α-helix	210-223	14
α-helix	224-231	8
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	303-304	2
α-helix	308-311	4
β-strand	317-318	2	6
α-helix	319	1
β-strand	323	1	8
β-strand	329	1	9
β-strand	330	1	8
β-strand	333	1	7
α-helix	336-338	3
α-helix	348	1
β-strand	349	1	9
α-helix	350-357	8
α-helix	389-407	19

Chain D: 16 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	1449-1450	2	10
α-helix	1451-1454	4
α-helix	32-33	2
β-strand	36-37	2	10
α-helix	39-62	24
α-helix	68-80	13
α-helix	90-92	3
α-helix	93-109	17
α-helix	114-133	20
α-helix	137-142	6
α-helix	157-161	5
α-helix	163-167	5
β-strand	183-187	5	11
α-helix	188-191	4
α-helix	192-195	4
β-strand	201-203	3	11
β-strand	206-210	5	11
α-helix	214-236	23
α-helix	237-239	3
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 polymerase alpha catalytic subunit, DNA primase large subunit	B, D	protein	269	HOMO SAPIENS	P49643 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4BPX_1 DNA PRIMASE SMALL SUBUNIT (chains A, C)
GTSMETFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRY
QSFNNQSDLEKEMQAANPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDD
VRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKL
SSAVRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENK
ESWDKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIM
LQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICREL
DAISTNEEEKEENEAESDVKHRTRDYKKTSLAPYVKVFEHFLENLDKSRKGELLKKSDLQ
KDF

Sequence of entity 2 (B, D), FASTA

>4BPX_2 DNA POLYMERASE ALPHA CATALYTIC SUBUNIT, DNA PRIMASE LARGE SUBUNIT (chains B, D)
MGYSEVNLSKLFAGCAVKSTGSTGSTGSTGSTGSNASYPHCLQFYLQPPSENISLIEFEN
LAIDRVKLLKSVENLGVSYVKGTEQYQSKLESELRKLKFSYRENLEDEYEPRRRDHISHF
ILRLAYCQSEELRRWFIQQEMDLLRFRFSILPKDKIQDFLKDSQLQFEAISDEEKTLREQ
EIVASSPSLSGLKLGFESIYKIPFADALDLFRGRKVYLEDGFAYVPLKDIVAIILNEFRA
KLSKALALTARSLPAVQSDERLQPLLNHL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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
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)

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