7SGZ: Yeast Rad24-RFC loader

Structure of the yeast Rad24-RFC loader bound to DNA and the closed 9-1-1 clamp. Determined by electron microscopy at 3.17 Å resolution. Released 23 Mar 2022.

Method: Electron microscopy
Resolution: 3.17 Å
Organisms: Saccharomyces cerevisiae, synthetic construct
Chains: 10
Atoms: 21,055
Mol. weight: 415.76 kDa
Ligands: MG, ADP, PO4, AGS
Released: 23 Mar 2022

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

Secondary structure: helices and β-sheets

7SGZ contains 134 α-helices and 98 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: 29 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	66-69	4
α-helix	82-95	14
β-strand	104-109	6	1
α-helix	117-124	8
α-helix	127-129	3
β-strand	148-150	3	1
α-helix	162-174	13
α-helix	182	1
β-strand	183-186	4	1
α-helix	189-191	3
α-helix	195-206	12
β-strand	219-224	6	1
β-strand	226	1	2
α-helix	227-230	4
β-strand	244	1	2
α-helix	246-249	4
α-helix	252-255	4
β-strand	260-264	5	1
α-helix	267-269	3
α-helix	270-283	14
α-helix	285-290	6
α-helix	297-307	11
α-helix	311-323	13
α-helix	335-337	3
α-helix	339-347	9
α-helix	356-366	11
α-helix	368-371	4
α-helix	376-383	8
α-helix	384-386	3
α-helix	394-407	14
α-helix	408-410	3
α-helix	414-430	17
α-helix	432-434	3
α-helix	446-467	22
α-helix	476-482	7
α-helix	487-494	8

Chain B: 20 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	27-39	13
β-strand	45-48	4	3
α-helix	56-67	12
α-helix	69-74	6
β-strand	78	1	3
α-helix	86-97	12
β-strand	109-114	6	3
α-helix	116-118	3
α-helix	121-134	14
β-strand	138-143	6	3
α-helix	147-149	3
α-helix	152-156	5
β-strand	159-162	4	3
α-helix	163-167	5
α-helix	168-182	15
β-strand	186	1	4
α-helix	188-198	11
α-helix	202-216	15
β-strand	219	1	4
α-helix	221-227	7
α-helix	232-240	9
α-helix	245-252	8
α-helix	253-257	5
α-helix	263-276	14
α-helix	282-301	20
α-helix	306-321	16

Chain C: 22 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
α-helix	31-43	13
β-strand	49-52	4	5
α-helix	59-71	13
β-strand	80-82	3	5
α-helix	90-92	3
α-helix	93-97	5
α-helix	98-100	3
β-strand	103	1	6
α-helix	110-111	2
β-strand	112-116	5	5
α-helix	119-121	3
α-helix	124-136	13
β-strand	141-147	7	5
α-helix	150-152	3
α-helix	155-160	6
β-strand	162-165	4	5
α-helix	167-169	3
α-helix	171-185	15
β-strand	188-189	2	7
α-helix	191-201	11
α-helix	205-218	14
β-strand	226-227	2	7
α-helix	229-236	8
α-helix	238-240	3
α-helix	241-253	13
α-helix	257-270	14
α-helix	274-285	12
α-helix	294-312	19
α-helix	316-330	15

Chain D: 24 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
α-helix	36-38	3
α-helix	43-53	11
β-strand	61-64	4	8
α-helix	71-82	12
α-helix	85-91	7
β-strand	92-95	4	8
α-helix	103-113	11
α-helix	117-119	3
α-helix	123-128	6
β-strand	135-139	5	8
α-helix	142-144	3
α-helix	147-159	13
β-strand	164-169	6	8
α-helix	178-183	6
β-strand	185-188	4	8
α-helix	189-191	3
α-helix	194-208	15
β-strand	212	1	9
α-helix	216-223	8
α-helix	229-245	17
α-helix	249-250	2
β-strand	251	1	9
α-helix	252	1
α-helix	253-259	7
α-helix	262-264	3
α-helix	265-276	12
α-helix	280-291	12
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	20-31	12
α-helix	33-35	3
β-strand	39-42	4	10
α-helix	49-60	12
β-strand	70	1	10
β-strand	73-76	4	11
β-strand	82-85	4	11
β-strand	88	1	10
β-strand	93-96	4	10
α-helix	106-117	12
β-strand	136-141	6	10
α-helix	143-145	3
α-helix	149-160	12
β-strand	165-171	7	10
α-helix	179-184	6
β-strand	186-189	4	10
α-helix	191-193	3
α-helix	195-209	15
β-strand	212	1	12
α-helix	217-225	9
α-helix	230-242	13
β-strand	247	1	12
α-helix	258-272	15
α-helix	276-290	15
α-helix	296-307	12
α-helix	315-334	20
α-helix	339-353	15

Chain F: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	13
α-helix	13-18	6
α-helix	20-29	10
β-strand	33-38	6	14
β-strand	42-46	5	14
β-strand	67	1	14
β-strand	70-71	2	14
β-strand	78-81	4	13
β-strand	93-95	3	14
α-helix	98-108	11
β-strand	120-124	5	13
β-strand	155-163	9	13
β-strand	200-207	8	13
α-helix	217-220	4
β-strand	231-233	3	14
α-helix	234-236	3
α-helix	241-256	16
β-strand	262-265	4	15
β-strand	282-286	5	15
β-strand	290-296	7	15
β-strand	409-411	3	15
α-helix	415-420	6
β-strand	429-434	6	14
β-strand	438-445	8	14
β-strand	462-464	3	14
β-strand	467-468	2	14

Chain G: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	13-15	3	15
α-helix	18-25	8
α-helix	26-28	3
β-strand	37-41	5	16
β-strand	45-52	8	16
β-strand	56-63	8	16
α-helix	64-66	3
β-strand	80-84	5	16
α-helix	86-94	9
β-strand	105-109	5	15
β-strand	117-122	6	15
β-strand	126-132	7	15
α-helix	149-151	3
β-strand	152-159	8	16
α-helix	160-173	14
β-strand	177-183	7	17
β-strand	191-197	7	17
β-strand	201-206	6	17
β-strand	214-219	6	16
β-strand	220	1	18
β-strand	227	1	18
β-strand	232-238	7	17
α-helix	239-248	10
β-strand	254-260	7	16
β-strand	265-270	6	16
β-strand	305-310	6	16
β-strand	313	1	6
α-helix	320-329	10

Chain H: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	17
α-helix	13-26	14
β-strand	29-34	6	19
β-strand	39-44	6	19
β-strand	50-56	7	19
α-helix	58-60	3
β-strand	92-97	6	19
α-helix	98-102	5
β-strand	115-120	6	17
β-strand	134-139	6	17
β-strand	145-150	6	17
α-helix	203-208	6
β-strand	230-231	2	19
α-helix	234-241	8
α-helix	246-248	3
β-strand	251-255	5	13
β-strand	262-266	5	13
β-strand	271	1	20
β-strand	277	1	20
β-strand	284-287	4	13
β-strand	295	1	19
β-strand	322-325	4	13
α-helix	327-338	12
α-helix	346-348	3
β-strand	349-351	3	19
β-strand	360-365	6	19
β-strand	369-375	7	19

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	460	Saccharomyces cerevisiae	Q02574
DNA damage checkpoint control protein RAD17	G	protein	401	Saccharomyces cerevisiae	P48581
DNA Damage Checkpoint protein DDC1	H	protein	593	Saccharomyces cerevisiae	Q08949
Watson strand	P	DNA	20	synthetic construct
Crick strand	T	DNA	40	synthetic construct

Sequence of entity 1 (A), FASTA

>7SGZ_1 Checkpoint protein RAD24 (chains A)
MDSTNLNKRPLLQYSLSSLGSQITKWSSSRPTSPVRKARSTENDFLSKQDTSSILPSIND
DGGEQWYEKFKPNCLEQVAIHKRKLKDVQEALDAMFLPNAKHRILLLSGPSGCSKSTVIK
ELSKILVPKYRQNSNGTSFRSTPNEHKVTEFRGDCIVNDLPQMESFSEFLKGARYLVMSN
LSLILIEDLPNVFHIDTRRRFQQLILQWLYSSEPLLPPLVICITECEIPENDNNYRKFGI
DYTFSAETIMNKEILMHPRLKRIKFNPINSTLLKKHLKFICVQNMKMLKEKNKWNKRQEV
IDYIAQETGDIRSAITTLQFWATSSGSLPISTRESTISYFHAIGKVIHGSHSTNNDNEMI
NNLFENSNNLLSKEDFKLGILENYNTFNKGEFSISDASSIVDCLSECDNMNGLPESNEYG
LREVRKTFRNISKQGHNHGTVYFPREWKVRKLQNSFKVQAEDWLNVSLYKYNAVHSFRNI
TLEFGYYAPLIRKCQSYKKKYILYYLKNLPSGSSGPKQTMDKFSDIMKVENGIDVVDRIG
GPIEALSVEDGLAPLMDNDSNNCDHLEDQKKERDRRLRMLIDQYERNVMMANDDLEDEET
SFNDDPIVDSDSDNSNNIGNETFGRSDEDESLCEILSQRQPRKAPVISESLSDSDLEIL

Sequence of entity 2 (B), FASTA

>7SGZ_2 Replication factor C subunit 4 (chains B)
MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH
CLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMT
AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIK
LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKML
LASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRIL
EGVGTYLQLASMLAKIHKLNNKA

Sequence of entity 3 (C), FASTA

>7SGZ_3 Replication factor C subunit 3 (chains C)
MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT
STIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEAD
AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIAN
VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPR
PSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLL
TKLADIEYSISKGGNDQIQGSAVIGAIKASFENETVKANV

Sequence of entity 4 (D), FASTA

>7SGZ_4 Replication factor C subunit 2 (chains D)
MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH
MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSK
PSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL
ASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK
GAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASV
VNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL

Sequence of entity 5 (E), FASTA

>7SGZ_5 Replication factor C subunit 5 (chains E)
MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI
FGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQME
QVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAP
IKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESM
ALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIIL
KELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD

Sequence of entity 6 (F), FASTA

>7SGZ_6 Mitosis Entry Checkpoint protein MEC3 (chains F)
MKLKLIVNGCEAPDDYKLLRTTINTVASLRKTAILRFNSERLTIISTPKSSLNSSNNGTI
LRGDTGQLWCTIPHDVFRLYTVISARELNTITMECNCDSLLSVFKRYDRVMNQGSSSNMT
IKLQSMPEWNTNNGTLSGGTAGGVDTTSKPNPICALGITFEEIVHTSGPNDAIVMNGGVD
EHNGLPTTVGTGNLLASNKVIMHSFKVPVKLLFRAQDTRIQEPMINYIQLMMYKLPPISG
EFGSAFHGFIRRVERYSNVNHIHLMGVKKKEHGNEGDDVELKIIVNELDWHLEICWNGPL
DSVIQRQEGLTDNPSQNQHIDTDGRQEEGSLPIIEADKPMSSLYTNTRDREMEENIRYDE
DLLRIEDSSIADTRGNIYTADTSGDTEFNDISVMVEKAEQESSSTHEVIIRCKDWKVCSK
LYAAFEEVVLAISHDESCVFHCSLDERGQIIYYIARSKGL

Sequence of entity 7 (G), FASTA

>7SGZ_7 DNA damage checkpoint control protein RAD17 (chains G)
MRINSELANKFSASTVHLEHITTALSCLTPFGSKDDVLIFIDADGLSFVRENNHVIKIQL
LLSRELFMSYSYRNETEDHMKLCVKINHILDSVSVMNRNSDDIVECTLSYDGHGSPFVLI
FEDSFISERVEYSTYLIKDFDTNGLELDRERISFEAIIKGEALHSALKDLKEIGCKECYV
YAKTEANDENVFALISKSQLGFSKIKLPSNRSILEKLQVFDGDSTTVIDGFAVIGFFDFT
SFDKIRKSTKIASKVLFRMDVHGVLSVNILSQTDDVIITDTTRPSNNRPGSIRQLQLPKD
YPGIVIEVCMLEKESIDEAAQTEIELLMETNELGNRNSFKKSTIRKRYGTDKGNETSNDN
LLQLNGKKIKLPSEEENNKNRESEDEENHCKYPTKDIPIFF

Sequence of entity 8 (H), FASTA

>7SGZ_8 DNA Damage Checkpoint protein DDC1 (chains H)
MSFKATITESGKQNIWFRAIYVLSTIQDDIKITVTTNELIAWSMNETDTTLCQVRFQKSF
FEEYEFKPHEIVFGENGVQVIEDTYGNSHKLYSFRVNGRHLTTISRKPDGDGIKSFTIAV
NNTSTCPESLANRLIVVIEMDSLIVKEYCPQFQPIKYDPIIINLKYKRRFLDVFGTAASD
RNPQEPLDPKLLDVFTNTERELTSALFNEEVESDIRKRNQLTAADEINYICCNSTLLKNF
LDNCNVNVTDEVKLEINVHRLSITAFTKAVYGKNNDLLRNALSMSNTISTLDLEHYCLFT
KSIIFKLKDFKNFITIGPSWKTTQDGNDNISLWFCHPGDPILMQMQKPGVKLELVEVTDS
NINDDILEGKFIKTAISGSKEEAGLKDNKESCESPLKSKTALKRENLPHSVAGTRNSPLK
VSYLTPDNGSTVAKTYRNNTARKLFVEEQSQSTNYEQDKRFRQASSVHMNMNREQSFDIG
TTHEVACPRNESNSLKRSIADICNETEDPTQQSTFAKRADTTVTWGKALPAADDEVSCSN
IDRKGMLKKEKLKHMQGLLNSQNDTSNHKKQDNKEMEDGLGLTQVEKPRGIFD

Sequence of entity 9 (P), FASTA

>7SGZ_9 Watson strand (chains P)
GCAGACACTACGAGTACATA

Sequence of entity 10 (T), FASTA

>7SGZ_10 Crick strand (chains T)
TTTTTTTTTTTATGTACTCGTAGTGTCTGCTTTTTTTTTT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
PO4	Phosphate ion	O4 P	1
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…
7SH2 3.23 Å, Structure of the yeast Rad24-RFC loader bound to DNA and the open 9-1-1 clamp

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