1SXJ: Eukaryotic Clamp Loader

Name: PDB 1SXJ: Crystal Structure of the Eukaryotic Clamp Loader (Replication Factor C, RFC) Bound to the DNA Sliding Clamp (Proliferating Cell Nuclear Antigen, PCNA)
Published: 2004-06-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: replication

Crystal Structure of the Eukaryotic Clamp Loader (Replication Factor C, RFC) Bound to the DNA Sliding Clamp (Proliferating Cell Nuclear Antigen, PCNA). Determined by X-ray diffraction at 2.85 Å resolution. Released 22 Jun 2004.

Method: X-ray diffraction
Resolution: 2.85 Å
Organism: Saccharomyces cerevisiae
Chains: 8
Atoms: 19,740
Mol. weight: 309.28 kDa
Ligands: ADP, AGS, MG
Released: 22 Jun 2004

Explore 1SXJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1SXJ contains 142 α-helices and 102 β-strands across 8 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: 32 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	298-301	4
α-helix	307-309	3
α-helix	314-325	12
α-helix	327-332	6
β-strand	348-352	5	1
α-helix	359-369	11
β-strand	373-377	5	1
α-helix	385-390	6
α-helix	392-395	4
β-strand	398	1	2
β-strand	419-423	5	1
α-helix	426-428	3
α-helix	436-446	11
β-strand	451-455	5	1
α-helix	464-466	3
β-strand	471-474	4	1
α-helix	480-494	15
α-helix	502-509	8
α-helix	514-521	8
α-helix	523-527	5
α-helix	535-542	8
α-helix	543-548	6
α-helix	550-558	9
β-strand	560	1	3
α-helix	561-563	3
α-helix	568-570	3
α-helix	574-581	8
α-helix	588-595	8
β-strand	600-601	2	3
α-helix	604-605	2
α-helix	610-631	22
α-helix	638-640	3
α-helix	641-645	5
α-helix	646-650	5
α-helix	651-654	4
β-strand	658-659	2	3
α-helix	669-687	19
α-helix	699-703	5
α-helix	707-714	8
α-helix	725-730	6
α-helix	737-746	10

Chain B: 25 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	20-22	3
α-helix	28-38	11
β-strand	45-48	4	4
α-helix	55-67	13
α-helix	68-70	3
α-helix	71-74	4
β-strand	75-78	4	4
α-helix	86-88	3
α-helix	89-93	5
α-helix	94-98	5
β-strand	99	1	5
β-strand	109-114	6	4
α-helix	116-118	3
α-helix	121-125	5
α-helix	128-133	6
β-strand	138-144	7	4
α-helix	147-149	3
α-helix	152-155	4
β-strand	159-162	4	4
α-helix	165-167	3
α-helix	168-182	15
β-strand	186	1	6
α-helix	188-198	11
α-helix	202-216	15
β-strand	219	1	6
α-helix	221-228	8
α-helix	233-240	8
α-helix	245-251	7
α-helix	252-257	6
α-helix	263-275	13
α-helix	282-300	19
α-helix	306-319	14

Chain C: 22 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	24-26	3
α-helix	31-42	12
β-strand	49-52	4	7
α-helix	59-71	13
α-helix	75-78	4
β-strand	79-82	4	7
α-helix	90-92	3
α-helix	93-97	5
α-helix	98-102	5
β-strand	103	1	8
β-strand	112-116	5	7
α-helix	119-121	3
α-helix	124-136	13
β-strand	141-147	7	7
α-helix	150-152	3
α-helix	155-158	4
β-strand	162-165	4	7
α-helix	167-170	4
α-helix	171-183	13
β-strand	189	1	9
α-helix	191-201	11
α-helix	205-211	7
β-strand	227	1	9
α-helix	229-235	7
α-helix	241-252	12
α-helix	256-268	13
α-helix	274-285	12
α-helix	293-310	18
α-helix	316-330	15

Chain D: 23 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
α-helix	46-52	7
β-strand	61-64	4	10
α-helix	71-88	18
β-strand	92-95	4	10
α-helix	103-105	3
α-helix	106-110	5
α-helix	111-115	5
α-helix	117-122	6
α-helix	125-128	4
β-strand	135-139	5	10
α-helix	142-144	3
α-helix	147-159	13
β-strand	164-170	7	10
α-helix	173-175	3
α-helix	178-183	6
β-strand	185-188	4	10
α-helix	194-206	13
α-helix	214-223	10
α-helix	228-237	10
α-helix	239-245	7
α-helix	253-260	8
α-helix	262-264	3
α-helix	266-276	11
α-helix	280-292	13
α-helix	300-310	11
α-helix	316-333	18
α-helix	339-352	14

Chain E: 17 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
α-helix	20-27	8
β-strand	39-42	4	11
α-helix	49-54	6
α-helix	56-60	5
β-strand	88-89	2	11
β-strand	93-96	4	11
α-helix	106-116	11
β-strand	136-141	6	11
α-helix	148-160	13
β-strand	165-171	7	11
α-helix	179-182	4
β-strand	186-189	4	11
α-helix	191-194	4
α-helix	195-209	15
β-strand	212-213	2	12
α-helix	217-226	10
α-helix	230-237	8
α-helix	239-242	4
β-strand	247-248	2	12
α-helix	258-272	15
α-helix	276-290	15
α-helix	296-305	10
α-helix	315-333	19
α-helix	338-353	16

Chain F: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	13
α-helix	11-22	12
β-strand	25-30	6	14
β-strand	34-40	7	14
β-strand	46-53	8	14
α-helix	54-56	3
β-strand	57-61	5	13
β-strand	66-71	6	14
α-helix	72-78	7
β-strand	87-92	6	13
β-strand	98-104	7	13
β-strand	110-117	8	13
α-helix	118-119	2
β-strand	135-139	5	14
α-helix	141-152	12
β-strand	157-163	7	15
β-strand	166-172	7	15
β-strand	176-182	7	15
β-strand	185-187	3	16
β-strand	190-195	6	16
β-strand	196-199	4	14
β-strand	203-208	6	15
α-helix	209-215	7
α-helix	218-220	3
β-strand	225-229	5	14
β-strand	235-241	7	14
β-strand	244-250	7	14
β-strand	253	1	8

Chain G: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	15
α-helix	9-17	9
β-strand	25-30	6	17
β-strand	34-40	7	17
β-strand	46-53	8	17
α-helix	54-56	3
β-strand	57-60	4	15
β-strand	66-71	6	17
α-helix	72-79	8
β-strand	87-92	6	15
β-strand	100-104	5	15
β-strand	110-116	7	15
β-strand	119	1	5
β-strand	135-140	6	17
α-helix	141-151	11
β-strand	157-162	6	18
β-strand	167-172	6	18
β-strand	176-182	7	18
β-strand	185	1	19
α-helix	191-193	3
β-strand	195	1	19
β-strand	196-199	4	17
β-strand	203-208	6	18
α-helix	209-215	7
α-helix	216-218	3
β-strand	224-229	6	17
β-strand	235-241	7	17
β-strand	244-250	7	17
β-strand	253	1	2

Chain H: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	0-6	7	18
α-helix	9-20	12
β-strand	25-30	6	20
β-strand	34-40	7	20
β-strand	47-53	7	20
α-helix	54-56	3
β-strand	57-60	4	18
β-strand	66-71	6	20
α-helix	72-79	8
β-strand	86-93	8	18
β-strand	98-105	8	18
β-strand	110-117	8	18
β-strand	119	1	20
α-helix	123-126	4
α-helix	131-133	3
β-strand	135-140	6	20
α-helix	141-151	11
β-strand	157-162	6	13
β-strand	167-172	6	13
β-strand	176-182	7	13
β-strand	186	1	21
β-strand	194	1	21
β-strand	196-199	4	20
β-strand	203-208	6	13
α-helix	209-215	7
α-helix	216-220	5
β-strand	224-229	6	20
α-helix	234	1
β-strand	235-240	6	20
β-strand	245-250	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Activator 1 95 kDa subunit	A	protein	516	Saccharomyces cerevisiae	P38630 (AlphaFold model)
Activator 1 37 kDa subunit	B	protein	323	Saccharomyces cerevisiae	P40339 (AlphaFold model)
Activator 1 40 kDa subunit	C	protein	340	Saccharomyces cerevisiae	P38629 (AlphaFold model)
Activator 1 41 kDa subunit	D	protein	353	Saccharomyces cerevisiae	P40348 (AlphaFold model)
Activator 1 40 kDa subunit	E	protein	354	Saccharomyces cerevisiae	P38251
Proliferating cell nuclear antigen	F, G, H	protein	283	Saccharomyces cerevisiae	P15873

Sequence of entity 1 (A), FASTA

>1SXJ_1 Activator 1 95 kDa subunit (chains A)
MGSSHHHHHHSSGLEVLFQGPHMASDKLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWEN
SKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLN
AGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTST
PLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQT
TRGDIRQVINLLSTISTTTKTINHENINEISKAWEKNIALKPFDIAHKMLDGQIYSDIGS
RNFTLNDKIALYFDDFDFTPLMIQENYLSTRPSVLKPGQSHLEAVAEAANCISLGDIVEK
KIRSSEQLWSLLPLHAVLSSVYPASKVAGHMAGRINFTAWLGQNSKSAKYYRLLQEIHYH
TRLGTSTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXFF
VGPDVTTAIIKKIPATVKSGFTRKYNSMTHPVAIYR

Sequence of entity 2 (B), FASTA

>1SXJ_2 Activator 1 37 kDa subunit (chains B)
MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH
CLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMT
AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIK
LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKML
LASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRIL
EGVGTYLQLASMLAKIHKLNNKA

Sequence of entity 3 (C), FASTA

>1SXJ_3 Activator 1 40 kDa subunit (chains C)
MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT
STIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEAD
AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIAN
VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPR
PSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLL
TKLADIEYSISKGGNDQIQGSAVIGAIKASFENETVKANV

Sequence of entity 4 (D), FASTA

>1SXJ_4 Activator 1 41 kDa subunit (chains D)
MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH
MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSK
PSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL
ASQCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK
GAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASV
VNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL

Sequence of entity 5 (E), FASTA

>1SXJ_5 Activator 1 40 kDa subunit (chains E)
MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI
FGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQME
QVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAP
IKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESM
ALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIIL
KELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD

Sequence of entity 6 (F, G, H), FASTA

>1SXJ_6 Proliferating cell nuclear antigen (chains F, G, H)
MGSSHHHHHHSSGLEVLFQGPHMASMLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGI
IAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNT
PDSIILLFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLS
DSINIMITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDI
IKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKFNDEE

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	4
MG	Magnesium ion	Mg	4

Primary citation

Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. Bowman, G.D., O'Donnell, M., Kuriyan, J. Nature (2004) 429:724-730. DOI 10.1038/nature02585 · PubMed

Other PDB entries of the same protein (UniProt P38630 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8DQX 2.1 Å, Open state of RFC:PCNA bound to a 3' ss/dsDNA junction
8DR1 2.14 Å, Consensus closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2)
8DR3 2.2 Å, Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD
8DR6 2.39 Å, Closed state of RFC:PCNA bound to a nicked dsDNA
8DR0 2.42 Å, Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction
8DR4 2.45 Å, Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) without NTD
9PEO 2.57 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
9PER 2.57 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
9PET 2.57 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
9PES 2.59 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
9PEU 2.62 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
9PEV 2.63 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…

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