7SH2: Yeast Rad24-RFC loader

Structure of the yeast Rad24-RFC loader bound to DNA and the open 9-1-1 clamp. Determined by electron microscopy at 3.23 Å resolution. Released 23 Mar 2022.

Method: Electron microscopy
Resolution: 3.23 Å
Organisms: Saccharomyces cerevisiae, synthetic construct
Chains: 10
Atoms: 20,933
Mol. weight: 416.87 kDa
Ligands: ADP, MG, AGS
Released: 23 Mar 2022

Explore 7SH2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SH2 contains 129 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: 26 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	66-69	4
α-helix	75-77	3
α-helix	82-96	15
β-strand	104-107	4	1
α-helix	116-126	11
α-helix	127-129	3
β-strand	148-150	3	1
α-helix	151-152	2
α-helix	163-174	12
α-helix	182	1
β-strand	183-185	3	1
α-helix	195-209	15
β-strand	219-222	4	1
β-strand	226	1	2
β-strand	244	1	2
α-helix	246-249	4
β-strand	260-262	3	1
α-helix	264-269	6
α-helix	270-283	14
α-helix	285-290	6
α-helix	298-307	10
α-helix	311-323	13
α-helix	339-347	9
α-helix	356-366	11
α-helix	368-372	5
α-helix	377-383	7
α-helix	384-386	3
α-helix	394-408	15
α-helix	414-431	18
α-helix	438-441	4
α-helix	447-470	24
α-helix	480-484	5
α-helix	487-494	8

Chain B: 21 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-14	4
α-helix	27-39	13
β-strand	45-48	4	3
α-helix	56-67	12
α-helix	69-72	4
β-strand	75	1	3
β-strand	78	1	3
α-helix	88-97	10
β-strand	109-114	6	3
α-helix	121-133	13
β-strand	138-143	6	3
α-helix	152-156	5
β-strand	159-162	4	3
α-helix	164-166	3
α-helix	168-182	15
β-strand	186	1	4
α-helix	188-198	11
α-helix	202-215	14
β-strand	219	1	4
α-helix	221-227	7
α-helix	229-231	3
α-helix	232-240	9
α-helix	245-252	8
α-helix	253-257	5
α-helix	258-259	2
α-helix	263-276	14
α-helix	282-301	20
α-helix	306-321	16

Chain C: 20 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	5
α-helix	60-70	11
α-helix	75-78	4
β-strand	80-82	3	5
α-helix	90-102	13
β-strand	103	1	6
α-helix	104-105	2
β-strand	112-116	5	5
α-helix	124-136	13
β-strand	141-147	7	5
α-helix	155-160	6
β-strand	162-165	4	5
α-helix	167-169	3
α-helix	171-185	15
β-strand	189	1	7
α-helix	191-201	11
α-helix	206-218	13
β-strand	227	1	7
α-helix	229-236	8
α-helix	238-240	3
α-helix	241-253	13
α-helix	257-269	13
α-helix	274-287	14
α-helix	295-312	18
α-helix	316-331	16

Chain D: 21 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
α-helix	44-53	10
β-strand	61-64	4	8
α-helix	71-82	12
α-helix	85-87	3
α-helix	88-91	4
β-strand	93-95	3	8
α-helix	103-113	11
α-helix	117-122	6
α-helix	123-126	4
β-strand	135-139	5	8
α-helix	142-144	3
α-helix	147-159	13
β-strand	164-170	7	8
α-helix	178-183	6
β-strand	185-188	4	8
α-helix	194-207	14
β-strand	212	1	9
α-helix	216-223	8
α-helix	228-245	18
β-strand	251	1	9
α-helix	253-260	8
α-helix	262-264	3
α-helix	265-276	12
α-helix	280-293	14
α-helix	297-310	14
α-helix	316-334	19
α-helix	339-351	13

Chain E: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	20-31	12
α-helix	33-35	3
β-strand	39-42	4	10
α-helix	49-60	12
β-strand	69-70	2	10
β-strand	73-78	6	11
β-strand	81-85	5	11
β-strand	88-90	3	10
β-strand	93-96	4	10
α-helix	104-117	14
β-strand	136-140	5	10
α-helix	150-160	11
β-strand	165-171	7	10
α-helix	179-184	6
β-strand	186-189	4	10
α-helix	191-193	3
α-helix	195-208	14
β-strand	212-213	2	12
α-helix	217-226	10
α-helix	230-243	14
β-strand	247-248	2	12
α-helix	258-272	15
α-helix	276-290	15
α-helix	296-308	13
α-helix	315-334	20
α-helix	339-353	15

Chain F: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	13
α-helix	13-29	17
β-strand	34-35	2	14
β-strand	36	1	15
β-strand	42-44	3	15
β-strand	70	1	16
β-strand	71-73	3	15
β-strand	78-81	4	13
β-strand	93-94	2	14
α-helix	98-108	11
β-strand	120-123	4	13
β-strand	156-163	8	13
β-strand	200-206	7	13
α-helix	215-219	5
β-strand	231-232	2	17
α-helix	240-255	16
β-strand	263-266	4	18
β-strand	281-286	6	18
β-strand	291-295	5	18
β-strand	409	1	18
α-helix	416-421	6
β-strand	429-430	2	16
β-strand	431-432	2	17
β-strand	433-434	2	19
β-strand	438-439	2	19
β-strand	442-444	3	16
β-strand	463-465	3	16
β-strand	468	1	19

Chain G: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	18
α-helix	18-25	8
α-helix	29-32	4
β-strand	37-41	5	20
β-strand	45-52	8	20
β-strand	56-63	8	20
β-strand	80-84	5	20
α-helix	86-95	10
β-strand	105-110	6	18
β-strand	117-123	7	18
β-strand	126-132	7	18
α-helix	149-151	3
β-strand	152-159	8	20
α-helix	160-171	12
β-strand	177-183	7	21
β-strand	191-193	3	21
β-strand	196-198	3	21
β-strand	201-207	7	21
β-strand	216-220	5	20
β-strand	227-228	2	20
β-strand	233-238	6	21
α-helix	239-248	10
β-strand	254-260	7	20
β-strand	265-270	6	20
β-strand	305-310	6	20
β-strand	313	1	6
α-helix	320-328	9

Chain H: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	21
α-helix	13-26	14
β-strand	29-35	7	22
β-strand	39-42	4	22
β-strand	50-56	7	22
α-helix	58-60	3
α-helix	68-70	3
α-helix	75-77	3
β-strand	78-79	2	22
β-strand	91-97	7	22
α-helix	98-102	5
α-helix	106-108	3
β-strand	113-120	8	21
β-strand	134-140	7	21
β-strand	145-150	6	21
β-strand	153	1	22
α-helix	203-208	6
β-strand	230-231	2	22
α-helix	235-242	8
α-helix	246-248	3
β-strand	251-255	5	23
β-strand	262-266	5	23
β-strand	283-285	3	23
β-strand	322-324	3	23
α-helix	327-333	7
α-helix	335-338	4
α-helix	346-348	3
β-strand	349-351	3	22
α-helix	359	1
β-strand	360-365	6	22
β-strand	369-375	7	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Checkpoint protein RAD24	A	protein	659	Saccharomyces cerevisiae	P32641 (AlphaFold model)
Replication factor C subunit 4	B	protein	323	Saccharomyces cerevisiae	P40339 (AlphaFold model)
Replication factor C subunit 3	C	protein	340	Saccharomyces cerevisiae	P38629 (AlphaFold model)
Replication factor C subunit 2	D	protein	353	Saccharomyces cerevisiae	P40348 (AlphaFold model)
Replication factor C subunit 5	E	protein	354	Saccharomyces cerevisiae	P38251
Mitosis Entry Checkpoint protein MEC3	F	protein	446	Saccharomyces cerevisiae	Q02574
DNA damage checkpoint control protein RAD17	G	protein	401	Saccharomyces cerevisiae	P48581
DNA damage checkpoint protein DDC1	H	protein	612	Saccharomyces cerevisiae	Q08949
Watson strand	P	DNA	20	synthetic construct
Crick strand	T	DNA	40	synthetic construct

Sequence of entity 1 (A), FASTA

>7SH2_1 Checkpoint protein RAD24 (chains A)
MDSTNLNKRPLLQYSLSSLGSQITKWSSSRPTSPVRKARSTENDFLSKQDTSSILPSIND
DGGEQWYEKFKPNCLEQVAIHKRKLKDVQEALDAMFLPNAKHRILLLSGPSGCSKSTVIK
ELSKILVPKYRQNSNGTSFRSTPNEHKVTEFRGDCIVNDLPQMESFSEFLKGARYLVMSN
LSLILIEDLPNVFHIDTRRRFQQLILQWLYSSEPLLPPLVICITECEIPENDNNYRKFGI
DYTFSAETIMNKEILMHPRLKRIKFNPINSTLLKKHLKFICVQNMKMLKEKNKWNKRQEV
IDYIAQETGDIRSAITTLQFWATSSGSLPISTRESTISYFHAIGKVIHGSHSTNNDNEMI
NNLFENSNNLLSKEDFKLGILENYNTFNKGEFSISDASSIVDCLSECDNMNGLPESNEYG
LREVRKTFRNISKQGHNHGTVYFPREWKVRKLQNSFKVQAEDWLNVSLYKYNAVHSFRNI
TLEFGYYAPLIRKCQSYKKKYILYYLKNLPSGSSGPKQTMDKFSDIMKVENGIDVVDRIG
GPIEALSVEDGLAPLMDNDSNNCDHLEDQKKERDRRLRMLIDQYERNVMMANDDLEDEET
SFNDDPIVDSDSDNSNNIGNETFGRSDEDESLCEILSQRQPRKAPVISESLSDSDLEIL

Sequence of entity 2 (B), FASTA

>7SH2_2 Replication factor C subunit 4 (chains B)
MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH
CLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMT
AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIK
LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKML
LASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRIL
EGVGTYLQLASMLAKIHKLNNKA

Sequence of entity 3 (C), FASTA

>7SH2_3 Replication factor C subunit 3 (chains C)
MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT
STIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEAD
AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIAN
VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPR
PSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLL
TKLADIEYSISKGGNDQIQGSAVIGAIKASFENETVKANV

Sequence of entity 4 (D), FASTA

>7SH2_4 Replication factor C subunit 2 (chains D)
MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH
MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSK
PSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL
ASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK
GAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASV
VNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL

Sequence of entity 5 (E), FASTA

>7SH2_5 Replication factor C subunit 5 (chains E)
MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI
FGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQME
QVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAP
IKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESM
ALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIIL
KELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD

Sequence of entity 6 (F), FASTA

>7SH2_6 Mitosis Entry Checkpoint protein MEC3 (chains F)
MKLKLIVNGCEAPDDYKLLRTTINTVASLRKTAILRFNSERLTIISTPKSSLNSSNNGTI
LRGDTGQLWCTIPHDVFRLYTVISARELNTITMECNCDSLLSVFKRYDRVMNQGSSSNMT
IKLQSCALGITFEEIVHTSGPNDAIVMNGGVDEHNGLPTTVGTGNLLASNKVIMHSFKVP
VKLLFRAQDTRIQEPMINYIQLMMYKLPPISGEFGSAFHGFIRRVERYSNVNHIHLMGVK
KKEHGNEGDDVELKIIVNELDWHLEICWNGPLDSVIQRQEGLTDNPSQNQHIDTDGRQEE
GSLPIIEADKPMSSLYTNTRDREMEENIRYDEDLLRIEDSSIADTRGNIYTADTSGDTEF
NDISVMVEKAEQESSSTHEVIIRCKDWKVCSKLYAAFEEVVLAISHDESCVFHCSLDRGS
LEDSEDVEKPRERGQIIYYIARSKGL

Sequence of entity 7 (G), FASTA

>7SH2_7 DNA damage checkpoint control protein RAD17 (chains G)
MRINSELANKFSASTVHLEHITTALSCLTPFGSKDDVLIFIDADGLSFVRENNHVIKIQL
LLSRELFMSYSYRNETEDHMKLCVKINHILDSVSVMNRNSDDIVECTLSYDGHGSPFVLI
FEDSFISERVEYSTYLIKDFDTNGLELDRERISFEAIIKGEALHSALKDLKEIGCKECYV
YAKTEANDENVFALISKSQLGFSKIKLPSNRSILEKLQVFDGDSTTVIDGFAVIGFFDFT
SFDKIRKSTKIASKVLFRMDVHGVLSVNILSQTDDVIITDTTRPSNNRPGSIRQLQLPKD
YPGIVIEVCMLEKESIDEAAQTEIELLMETNELGNRNSFKKSTIRKRYGTDKGNETSNDN
LLQLNGKKIKLPSEEENNKNRESEDEENHCKYPTKDIPIFF

Sequence of entity 8 (H), FASTA

>7SH2_8 DNA damage checkpoint protein DDC1 (chains H)
MSFKATITESGKQNIWFRAIYVLSTIQDDIKITVTTNELIAWSMNETDTTLCQVRFQKSF
FEEYEFKPHEIVFGENGVQVIEDTYGNSHKLYSFRVNGRHLTTISRKPDGDGIKSFTIAV
NNTSTCPESLANRLIVVIEMDSLIVKEYCPQFQPIKYDPIIINLKYKRRFLDVFGTAASD
RNPQEPLDPKLLDVFTNTERELTSALFNEEVESDIRKRNQLTAADEINYICCNSTLLKNF
LDNCNVNVTDEVKLEINVHRLSITAFTKAVYGKNNDLLRNALSMSNTISTLDLEHYCLFT
TIEDEKQDKRSHSKRREHMKSIIFKLKDFKNFITIGPSWKTTQDGNDNISLWFCHPGDPI
LMQMQKPGVKLELVEVTDSNINDDILEGKFIKTAISGSKEEAGLKDNKESCESPLKSKTA
LKRENLPHSVAGTRNSPLKVSYLTPDNGSTVAKTYRNNTARKLFVEEQSQSTNYEQDKRF
RQASSVHMNMNREQSFDIGTTHEVACPRNESNSLKRSIADICNETEDPTQQSTFAKRADT
TVTWGKALPAADDEVSCSNIDRKGMLKKEKLKHMQGLLNSQNDTSNHKKQDNKEMEDGLG
LTQVEKPRGIFD

Sequence of entity 9 (P), FASTA

>7SH2_9 Watson strand (chains P)
GCAGACACTACGAGTACATA

Sequence of entity 10 (T), FASTA

>7SH2_10 Crick strand (chains T)
TTTTTTTTTTTATGTACTCGTAGTGTCTGCTTTTTTTTTT

Ligands and cofactors

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

Primary citation

DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp. Zheng, F., Georgescu, R.E., Yao, N.Y. et al. Nat Struct Mol Biol (2022) 29:376-385. DOI 10.1038/s41594-022-00742-6 · PubMed

Other PDB entries of the same protein (UniProt P32641 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8DQW 2.1 Å, Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
7ST9 2.2 Å, Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
7STB 2.72 Å, Closed state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
7STE 2.73 Å, Rad24-RFC ADP state
8FS5 2.76 Å, Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in…
8FS7 2.85 Å, Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in…
8FS6 2.9 Å, Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in…
8FS3 2.93 Å, Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in…
8FS4 2.94 Å, Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in…
8FS8 3.04 Å, Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 5-nt gapped DNA…
7SGZ 3.17 Å, Structure of the yeast Rad24-RFC loader bound to DNA and the closed 9-1-1 clamp

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