7JPQ: Origin recognition complex subunit 2

ORC-O2-5: Human Origin Recognition Complex (ORC) with subunits 2,3,4,5. Determined by electron microscopy at 3.5 Å resolution. Released 2 Sept 2020.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 13,863
Mol. weight: 250.36 kDa
Ligands: MG, ATP
Released: 2 Sept 2020

Explore 7JPQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7JPQ contains 94 α-helices and 31 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 B: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	270-275	6
α-helix	285-291	7
α-helix	298-306	9
β-strand	310-314	5	1
α-helix	320-329	10
β-strand	336-339	4	1
α-helix	348-355	8
α-helix	356-360	5
α-helix	369-378	10
β-strand	388-392	5	1
α-helix	403-413	11
β-strand	418-424	7	1
α-helix	429-432	4
α-helix	435-441	7
β-strand	443-447	5	1
α-helix	474-482	9
α-helix	486-499	14
β-strand	511	1	2
α-helix	513-521	9
α-helix	529-541	13
β-strand	546	1	3
β-strand	557	1	2
β-strand	558	1	3
α-helix	563-567	5

Chain C: 33 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	1
α-helix	26-30	5
α-helix	40-65	26
α-helix	67-87	21
β-strand	101-106	6	4
α-helix	114-128	15
β-strand	133-136	4	4
α-helix	144-157	14
α-helix	181-191	11
α-helix	213-214	2
β-strand	215-219	5	4
α-helix	227-239	13
β-strand	246-252	7	4
α-helix	257-262	6
α-helix	265-268	4
β-strand	272-277	6	4
α-helix	281-292	12
α-helix	304-312	9
α-helix	313-317	5
α-helix	321-337	17
α-helix	340-344	5
α-helix	348-356	9
α-helix	360-368	9
α-helix	370-377	8
α-helix	383-389	7
α-helix	391-425	35
α-helix	435-444	10
α-helix	451-461	11
α-helix	465-481	17
α-helix	488-497	10
α-helix	548-566	19
α-helix	570-572	3
α-helix	576-578	3
α-helix	584-591	8
α-helix	600-603	4
α-helix	606-608	3
α-helix	630-637	8
α-helix	645-656	12
α-helix	673-689	17

Chain D: 22 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	19-28	10
α-helix	41-56	16
β-strand	61-66	6	5
α-helix	73-85	13
α-helix	88-91	4
β-strand	95-100	6	5
α-helix	107-117	11
α-helix	132-141	10
β-strand	154-159	6	5
α-helix	161-164	4
α-helix	171-179	9
β-strand	187-193	7	5
α-helix	198-200	3
α-helix	204-209	6
β-strand	214-216	3	5
α-helix	223-233	11
α-helix	236-237	2
α-helix	243-257	15
α-helix	260-270	11
α-helix	276-287	12
α-helix	299-309	11
α-helix	313-320	8
α-helix	323-339	17
β-strand	344	1	6
α-helix	346-357	12
α-helix	369-381	13
β-strand	385-387	3	6
β-strand	402-404	3	6
α-helix	408-416	9
α-helix	423-430	8

Chain E: 24 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-22	11
β-strand	32-36	5	7
α-helix	43-54	12
β-strand	58-62	5	7
α-helix	69-81	13
α-helix	99-109	11
β-strand	120-125	6	7
α-helix	127-132	6
α-helix	137-142	6
α-helix	144-148	5
β-strand	152-158	7	7
α-helix	162-165	4
α-helix	172-174	3
β-strand	175-178	4	7
α-helix	180-182	3
α-helix	184-191	8
α-helix	201-215	15
α-helix	222-231	10
α-helix	233-236	4
α-helix	238-241	4
α-helix	250-266	17
α-helix	275-282	8
α-helix	304-317	14
α-helix	321-323	3
α-helix	324-327	4
β-strand	357-358	2	8
α-helix	359-369	11
α-helix	378-389	12
β-strand	393-395	3	8
β-strand	406-409	4	8
α-helix	413-422	10
α-helix	427-430	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Origin recognition complex subunit 2	B	protein	577	Homo sapiens	Q13416 (AlphaFold model)
Origin recognition complex subunit 3	C	protein	712	Homo sapiens	Q9UBD5 (AlphaFold model)
Origin recognition complex subunit 4	D	protein	436	Homo sapiens	O43929 (AlphaFold model)
Origin recognition complex subunit 5	E	protein	435	Homo sapiens	O43913 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>7JPQ_1 Origin recognition complex subunit 2 (chains B)
MSKPELKEDKMLEVHFVGDDDVLNHILDREGGAKLKKERAQLLVNPKKIIKKPEYDLEED
DQEVLKDQNYVEIMGRDVQESLKNGSATGGGNKVYSFQNRKHSEKMAKLASELAKTPQKS
VSFSLKNDPEITINVPQSSKGHSASDKVQPKNNDKSEFLSTAPRSLRKRLIVPRSHSDSE
SEYSASNSEDDEGVAQEHEEDTNAVIFSQKIQAQNRVVSAPVGKETPSKRMKRDKTSDLV
EEYFEAHSSSKVLTSDRTLQKLKRAKLDQQTLRNLLSKVSPSFSAELKQLNQQYEKLFHK
WMLQLHLGFNIVLYGLGSKRDLLERFRTTMLQDSIHVVINGFFPGISVKSVLNSITEEVL
DHMGTFRSILDQLDWIVNKFKEDSSLELFLLIHNLDSQMLRGEKSQQIIGQLSSLHNIYL
IASIDHLNAPLMWDHAKQSLFNWLWYETTTYSPYTEETSYENSLLVKQSGSLPLSSLTHV
LRSLTPNARGIFRLLIKYQLDNQDNPSYIGLSFQDFYQQCREAFLVNSDLTLRAQLTEFR
DHKLIRTKKGTDGVEYLLIPVDNGTLTDFLEKEEEEA

Sequence of entity 2 (C), FASTA

>7JPQ_2 Origin recognition complex subunit 3 (chains C)
MATSSMSKGCFVFKPNSKKRKISLPIEDYFNKGKNEPEDSKLRFETYQLIWQQMKSENER
LQEELNKNLFDNLIEFLQKSHSGFQKNSRDLGGQIKLREIPTAALVLGVNVTDHDLTFGS
LTEALQNNVTPYVVSLQAKDCPDMKHFLQKLISQLMDCCVDIKSKEEESVHVTQRKTHYS
MDSLSSWYMTVTQKTDPKMLSKKRTTSSQWQSPPVVVILKDMESFATKVLQDFIIISSQH
LHEFPLILIFGIATSPIIIHRLLPHAVSSLLCIELFQSLSCKEHLTTVLDKLLLTTQFPF
KINEKVLQVLTNIFLYHDFSVQNFIKGLQLSLLEHFYSQPLSVLCCNLPEAKRRINFLSN
NQCENIRRLPSFRRYVEKQASEKQVALLTNERYLKEETQLLLENLHVYHMNYFLVLRCLH
KFTSSLPKYPLGRQIRELYCTCLEKNIWDSEEYASVLQLLRMLAKDELMTILEKCFKVFK
SYCENHLGSTAKRIEEFLAQFQSLDAETKEEEDASGSQPKGLQKTDLYHLQKSLLEMKEL
RRSKKQTKFEVLRENVVNFIDCLVREYLLPPETQPLHEVVYFSAAHALREHLNAAPRIAL
HTALNNPYYYLKNEALKSEEGCIPNIAPDICIAYKLHLECSRLINLVDWSEAFATVVTAA
EKMDANSATSEEMNEIIHARFIRAVSELELLGFIKPTKQKTDHVARLTWGGC

Sequence of entity 3 (D), FASTA

>7JPQ_3 Origin recognition complex subunit 4 (chains D)
MSSRKSKSNSLIHTECLSQVQRILRERFCRQSPHSNLFGVQVQYKHLSELLKRTALHGES
NSVLIIGPRGSGKTMLINHALKELMEIEEVSENVLQVHLNGLLQINDKIALKEITRQLNL
ENVVGDKVFGSFAENLSFLLEALKKGDRTSSCPVIFILDEFDLFAHHKNQTLLYNLFDIS
QSAQTPIAVIGLTCRLDILELLEKRVKSRFSHRQIHLMNSFGFPQYVKIFKEQLSLPAEF
PDKVFAEKWNENVQYLSEDRSVQEVLQKHFNISKNLRSLHMLLMLALNRVTASHPFMTAV
DLMEASQLCSMDSKANIVHGLSVLEICLIIAMKHLNDIYEEEPFNFQMVYNEFQKFVQRK
AHSVYNFEKPVVMKAFEHLQQLELIKPMERTSGNSQREYQLMKLLLDNTQIMNALQKYPN
CPTDVRQWATSSLSWL

Sequence of entity 4 (E), FASTA

>7JPQ_4 Origin recognition complex subunit 5 (chains E)
MPHLENVVLCRESQVSILQSLFGERHHFSFPSIFIYGHTASGKTYVTQTLLKTLELPHVF
VNCVECFTLRLLLEQILNKLNHLSSSEDGCSTEITCETFNDFVRLFKQVTTAENLKDQTV
YIVLDKAEYLRDMEANLLPGFLRLQELADRNVTVLFLSEIVWEKFRPNTGCFEPFVLYFP
DYSIGNLQKILSHDHPPEYSADFYAAYINILLGVFYTVCRDLKELRHLAVLNFPKYCEPV
VKGEASERDTRKLWRNIEPHLKKAMQTVYLREISSSQWEKLQKDDTDPGQLKGLSAHTHV
ELPYYSKFILIAAYLASYNPARTDKRFFLKHHGKIKKTNFLKKHEKTSNHLLGPKPFPLD
RLLAILYSIVDSRVAPTANIFSQITSLVTLQLLTLVGHDDQLDGPKYKCTVSLDFIRAIA
RTVNFDIIKYLYDFL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

The dynamic nature of the human Origin Recognition Complex revealed through five cryoEM structures. Jaremko, M.J., On, K.F., Thomas, D.R. et al. Elife (2020) 9. DOI 10.7554/eLife.58622 · PubMed

Other PDB entries of the same protein (UniProt Q13416 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5C8H 2.01 Å, Crystal structure of ORC2 C-terminal domain
11RL 2.8 Å, CryoEM structure of the human origin recognition complex with DNA and CDC6 protein
7JPO 3.2 Å, ORC-O1AAA: Human Origin Recognition Complex (ORC) with dynamic/unresolved ORC2 WH
8S0D 3.6 Å, H. sapiens MCM bound to double stranded DNA and ORC1-6
7JPP 3.7 Å, ORC-O2WH: Human Origin Recognition Complex (ORC) with dynamic/unresolved ORC1 AAA+ domain
7CTE 3.8 Å, Human Origin Recognition Complex, ORC2-5
8S0E 3.8 Å, H. sapiens OCCM bound to double stranded DNA
7JPR 4.0 Å, ORC-OPEN: Human Origin Recognition Complex (ORC) in an open conformation
8S0C 4.0 Å, H. sapiens ORC1-5 bound to double stranded DNA as part of the MCM-ORC complex
8S0F 4.1 Å, H. sapiens OC1M bound to double stranded DNA
7JPS 4.4 Å, ORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in the core
7CTF 4.8 Å, Human origin recognition complex 1-5 State II

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