7Z6H: Cell cycle checkpoint control protein RAD9A

Structure of DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp. Determined by electron microscopy at 3.59 Å resolution. Released 4 May 2022.

Method: Electron microscopy
Resolution: 3.59 Å
Organisms: Homo sapiens, synthetic construct
Chains: 10
Atoms: 20,629
Mol. weight: 516.75 kDa
Ligands: AGS
Released: 4 May 2022

Explore 7Z6H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z6H contains 121 α-helices and 95 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: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	9-23	15
β-strand	26-32	7	2
β-strand	35-41	7	2
β-strand	48-53	6	2
β-strand	60	1	1
β-strand	73-76	4	2
α-helix	77-86	10
β-strand	96-101	6	1
β-strand	108-109	2	1
β-strand	112-113	2	3
β-strand	119-122	4	3
β-strand	123-124	2	1
β-strand	127	1	2
α-helix	130-132	3
β-strand	144-148	5	2
α-helix	149-155	7
β-strand	166-171	6	4
β-strand	175-180	6	4
β-strand	195-198	4	4
β-strand	206-208	3	2
β-strand	214-217	4	4
α-helix	220-229	10
β-strand	235-239	5	2
α-helix	246-247	2
β-strand	248-252	5	2
β-strand	257-261	5	2

Chain B: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	16-21	6	5
α-helix	24-32	9
β-strand	39-41	3	6
β-strand	44	1	7
β-strand	45	1	8
β-strand	48-49	2	8
β-strand	52-55	4	6
β-strand	59-63	5	6
β-strand	65-66	2	8
β-strand	72-74	3	5
β-strand	80	1	7
β-strand	83-85	3	6
α-helix	86-93	8
β-strand	107-112	6	5
β-strand	119-125	7	5
β-strand	128-134	7	5
β-strand	152-158	7	6
α-helix	164-168	5
β-strand	176-181	6	3
β-strand	188-192	5	3
β-strand	199-203	5	3
β-strand	210-213	4	6
β-strand	219-224	6	3
α-helix	225-228	4
α-helix	231-236	6
β-strand	241-246	6	6
β-strand	251-255	5	6
β-strand	257-258	2	9
β-strand	264-265	2	9
β-strand	267-271	5	6

Chain C: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	4
α-helix	10-26	17
β-strand	29-34	6	10
β-strand	38-43	6	10
β-strand	53-59	7	10
β-strand	66-70	5	4
β-strand	79-84	6	10
α-helix	85-93	9
β-strand	100-106	7	4
β-strand	112-119	8	4
α-helix	126	1
β-strand	127-134	8	4
β-strand	136-137	2	10
α-helix	138-139	2
α-helix	140-146	7
α-helix	148-150	3
β-strand	156-159	4	10
α-helix	163-174	12
β-strand	180-184	5	5
β-strand	190-195	6	5
β-strand	199-205	7	5
α-helix	208-211	4
β-strand	230-232	3	5
α-helix	237-243	7
β-strand	252-255	4	10
β-strand	260-267	8	10
β-strand	270-277	8	10

Chain D: 21 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	40-43	4
α-helix	49-51	3
α-helix	56-66	11
β-strand	74-77	4	11
α-helix	85-95	11
β-strand	105-108	4	11
α-helix	116-118	3
α-helix	119-123	5
α-helix	124-127	4
β-strand	145-149	5	11
α-helix	152-154	3
α-helix	157-169	13
β-strand	174-180	7	11
α-helix	183-185	3
α-helix	188-191	4
β-strand	195-198	4	11
α-helix	204-218	15
α-helix	224-233	10
α-helix	238-252	15
α-helix	259-266	8
α-helix	268-270	3
α-helix	271-282	12
α-helix	286-298	13
α-helix	303-314	12
α-helix	321-339	19
α-helix	345-359	15

Chain E: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	21-30	10
α-helix	35-37	3
β-strand	38-41	4	12
α-helix	48-59	12
β-strand	70-75	6	13
β-strand	81-86	6	13
β-strand	93-95	3	12
α-helix	104-117	14
β-strand	130-135	6	12
α-helix	142-154	13
β-strand	159-164	6	12
α-helix	173-176	4
β-strand	182-183	2	12
α-helix	190-201	12
α-helix	209-218	10
α-helix	223-236	14
α-helix	250-264	15
α-helix	268-283	16
α-helix	288-300	13
α-helix	306-324	19
α-helix	328-347	20

Chain F: 17 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	38-41	4
α-helix	55-66	12
β-strand	72-75	4	14
α-helix	82-94	13
β-strand	102-105	4	14
α-helix	114-125	12
β-strand	136-141	6	14
α-helix	143-145	3
α-helix	148-157	10
α-helix	161-163	3
β-strand	165-170	6	14
α-helix	179-182	4
β-strand	186-189	4	14
α-helix	195-209	15
α-helix	215-225	11
α-helix	229-241	13
α-helix	248-253	6
α-helix	260-271	12
α-helix	275-288	14
α-helix	292-304	13
α-helix	310-329	20
α-helix	334-348	15

Chain G: 22 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	31-33	3
α-helix	39-49	11
β-strand	56-59	4	15
α-helix	66-77	12
β-strand	87-90	4	15
α-helix	99-102	4
α-helix	104-109	6
α-helix	112-113	2
β-strand	120-125	6	15
α-helix	127-129	3
α-helix	132-144	13
β-strand	149-155	7	15
α-helix	165-167	3
β-strand	170	1	15
β-strand	173	1	15
α-helix	175-177	3
α-helix	179-192	14
α-helix	199-207	9
α-helix	214-224	11
α-helix	232-239	8
α-helix	241-243	3
α-helix	244-256	13
α-helix	259-272	14
α-helix	278-290	13
α-helix	296-310	15
α-helix	311-313	3
α-helix	318-335	18

Chain K: 27 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	91-94	4
α-helix	100-102	3
α-helix	107-122	16
β-strand	132-136	5	16
α-helix	143-153	11
β-strand	157-159	3	16
α-helix	162-164	3
α-helix	192-205	14
β-strand	221-225	5	16
α-helix	230-235	6
α-helix	238-249	12
β-strand	254-257	4	16
α-helix	266-271	6
α-helix	276-280	5
β-strand	282	1	16
β-strand	285-286	2	16
α-helix	289-291	3
α-helix	292-308	17
α-helix	316-318	3
α-helix	319-327	9
α-helix	333-343	11
α-helix	390-392	3
α-helix	396-405	10
β-strand	408	1	17
α-helix	424-426	3
β-strand	431	1	17
α-helix	435-441	7
α-helix	446-456	11
α-helix	464-479	16
α-helix	492-505	14
α-helix	529-544	16
α-helix	556	1
α-helix	557-561	5
α-helix	562-566	5
α-helix	576-583	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell cycle checkpoint control protein RAD9A	A	protein	405	Homo sapiens	Q99638 (AlphaFold model)
Cell cycle checkpoint protein RAD1,Cell cycle checkpoint protein RAD17	B, K	protein	1021	Homo sapiens	O60671 (AlphaFold model), O75943 (AlphaFold model)
Checkpoint protein HUS1	C	protein	280	Homo sapiens	O60921 (AlphaFold model)
Replication factor C subunit 4	D	protein	363	Homo sapiens	P35249
Replication factor C subunit 3	E	protein	356	Homo sapiens	P40938
Replication factor C subunit 2	F	protein	354	Homo sapiens	P35250
Replication factor C subunit 5	G	protein	360	Homo sapiens	P40937
Hairpin DNA	X, Y	DNA	77	synthetic construct

Sequence of entity 1 (A), FASTA

>7Z6H_1 Cell cycle checkpoint control protein RAD9A (chains A)
MKCLVTGGNVKVLGKAVHSLSRIGDELYLEPLEDGLSLRTVNSSRSAYACFLFAPLFFQQ
YQAATPGQDLLRCKILMKSFLSVFRSLAMLEKTVEKCCISLNGRSSRLVVQLHCKFGVRK
THNLSFQDCESLQAVFDPASCPHMLRAPARVLGEAVLPFSPALAEVTLGIGRGRRVILRS
YHEEEADSTAKAMVTEMCLGEEDFQQLQAQEGVAITFCLKEFRGLLSFAESANLNLSIHF
DAPGRPAIFTIKDSLLDGHFVLATLSDTDSHSQDLGSPERHQPVPQLQAHSTPHPDDFAN
DDIDSYMIAMETTIGNEGSRVLPSISLSPGPQPPKSPGPHSEEEDEAEPSTVPGTPPPKK
FRSLFFGSILAPVRSPQGPSPVLAEDSEGEGTSAGSRHHHHHHHH

Sequence of entity 2 (B, K), FASTA

>7Z6H_2 Cell cycle checkpoint protein RAD1,Cell cycle checkpoint protein RAD17 (chains B, K)
MPLLTQQIQDEDDQYSLVASLDNVRNLSTILKAIHFREHATCFATKNGIKVTVENAKCVQ
ANAFIQAGIFQEFKVQEESVTFRINLTVLLDCLSIFGSSPMPGTLTALRMCYQGYGYPLM
LFLEEGGVVTVCKINTQEPEETLDFDFCSTNVINKIILQSEGLREAFSELDMTSEVLQIT
MSPDKPYFRLSTFGNAGSSHLDYPKDSDLMEAFHCNQTQVNRYKISLLKPSTKALVLSCK
VSIRTDNRGFLSLQYMIRNEDGQICFVEYYCCPDEEVPESESGRGSMSAWSHPQFEKGSA
GSAAGSGAGWSHPQFEKLEVLFQGPGHMSKTFLRPKVSSTKVTDWVDPSFDDFLECSGVS
TITATSLGVNNSSHRRKNGPSTLESSRFPARKRGNLSSLEQIYGLENSKEYLSENEPWVD
KYKPETQHELAVHKKKIEEVETWLKAQVLERQPKQGGSILLITGPPGCGKTTTLKILSKE
HGIQVQEWINPVLPDFQKDDFKGMFNTESSFHMFPYQSQIAVFKEFLLRATKYNKLQMLG
DDLRTDKKIILVEDLPNQFYRDSHTLHEVLRKYVRIGRCPLIFIISDSLSGDNNQRLLFP
KEIQEECSISNISFNPVAPTIMMKFLNRIVTIEANKNGGKITVPDKTSLELLCQGCSGDI
RSAINSLQFSSSKGENNLRPRKKGMSLKSDAVLSKSKRRKKPDRVFENQEVQAIGGKDVS
LFLFRALGKILYCKRASLTELDSPRLPSHLSEYERDTLLVEPEEVVEMSHMPGDLFNLYL
HQNYIDFFMEIDDIVRASEFLSFADILSGDWNTRSLLREYSTSIATRGVMHSNKARGYAH
CQGGGSSFRPLHKPQWFLINKKYRENCLAAKALFPDFCLPALCLQTQLLPYLALLTIPMR
NQAQISFIQDIGRLPLKRHFGRLKMEALTDREHGMIDPDSGDEAQLNGGHSAEESLGEPT
QATVPETWSLPLSQNSASELPASQPQPFSAQGDMEENIIIEDYESDGTLEGASHHHHHHH
H

Sequence of entity 3 (C), FASTA

>7Z6H_3 Checkpoint protein HUS1 (chains C)
MKFRAKIVDGACLNHFTRISNMIAKLAKTCTLRISPDKLNFILCDKLANGGVSMWCELEQ
ENFFNEFQMEGVSAENNEIYLELTSENLSRALKTAQNARALKIKLTNKHFPCLTVSVELL
SMSSSSRIVTHDIPIKVIPRKLWKDLQEPVVPDPDVSIYLPVLKTMKSVVEKMKNISNHL
VIEANLDGELNLKIETELVCVTTHFKDLGNPPLASESTHEDRNVEHMAEVHIDIRKLLQF
LAGQQVNPTKALCNIVNNKMVHFDLLHEDVSLQYFIPALS

Sequence of entity 4 (D), FASTA

>7Z6H_4 Replication factor C subunit 4 (chains D)
MQAFLKGTSISTKPPLTKDRGVAASAGSSGENKKAKPVPWVEKYRPKCVDEVAFQEEVVA
VLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELFGPELFRLRVLELNASDERGIQVVR
EKVKNFAQLTVSGSRSDGKPCPPFKIVILDEADSMTSAAQAALRRTMEKESKTTRFCLIC
NYVSRIIEPLTSRCSKFRFKPLSDKIQQQRLLDIAKKENVKISDEGIAYLVKVSEGDLRK
AITFLQSATRLTGGKEITEKVITDIAGVIPAEKIDGVFAACQSGSFDKLEAVVKDLIDEG
HAATQLVNQLHDVVVENNLSDKQKSIITEKLAEVDKCLADGADEHLQLISLCATVMQQLS
QNS

Sequence of entity 5 (E), FASTA

>7Z6H_5 Replication factor C subunit 3 (chains E)
MSLWVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCILRELY
GVGVEKLRIEHQTITTPSKKKIEISTIASNYHLEVNPSDAGNSDRVVIQEMLKTVAQSQQ
LETNSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCL
AVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCEACRVQQYPF
TADQEIPETDWEVYLRETANAIVSQQTPQRLLEVRGRLYELLTHCIPPEIIMKGLLSELL
HNCDGQLKGEVAQMAAYYEHRLQLGSKAIYHLEAFVAKFMALYKKFMEDGLEGMMF

Sequence of entity 6 (F), FASTA

>7Z6H_6 Replication factor C subunit 2 (chains F)
MEVEAVCGGAGEVEAQDSDPAPAFSKAPGSAGHYELPWVEKYRPVKLNEIVGNEDTVSRL
EVFAREGNVPNIIIAGPPGTGKTTSILCLARALLGPALKDAMLELNASNDRGIDVVRNKI
KMFAQQKVTLPKGRHKIIILDEADSMTDGAQQALRRTMEIYSKTTRFALACNASDKIIEP
IQSRCAVLRYTKLTDAQILTRLMNVIEKERVPYTDDGLEAIIFTAQGDMRQALNNLQSTF
SGFGFINSENVFKVCDEPHPLLVKEMIQHCVNANIDEAYKILAHLWHLGYSPEDIIGNIF
RVCKTFQMAEYLKLEFIKEIGYTHMKIAEGVNSLLQMAGLLARLCQKTMAPVAS

Sequence of entity 7 (G), FASTA

>7Z6H_7 Replication factor C subunit 5 (chains G)
MGSHHHHHHSAALEVLFQGPGETSALKQQEQPAATKIRNLPWVEKYRPQTLNDLISHQDI
LSTIQKFINEDRLPHLLLYGPPGTGKTSTILACAKQLYKDKEFGSMVLELNASDDRGIDI
IRGPILSFASTRTIFKKGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYLSK
IIPALQSRCTRFRFGPLTPELMVPRLEHVVEEEKVDISEDGMKALVTLSSGDMRRALNIL
QSTNMAFGKVTEETVYTCTGHPLKSDIANILDWMLNQDFTTAYRNITELKTLKGLALHDI
LTEIHLFVHRVDFPSSVRIHLLTKMADIEYRLSVGTNEKIQLSSLIAAFQVTRDLIVAEA

Sequence of entity 8 (X, Y), FASTA

>7Z6H_8 Hairpin DNA (chains X, Y)
CCCGTATATTCTCCTACAGCACTAAATAATAGTGCTGTAGGAGAATATACGGGCTGCTCG
TGTTGACAAGTACTGAT

Ligands and cofactors

ID	Name	Formula	Copies
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	5

Primary citation

Structure of the human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp bound to a dsDNA-ssDNA junction. Day, M., Oliver, A.W., Pearl, L.H. Nucleic Acids Res (2022) 50:8279-8289. DOI 10.1093/nar/gkac588 · PubMed

Other PDB entries of the same protein (UniProt Q99638 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JZY 1.5 Å, RPA70N-RAD9 fusion
8GNN 2.12 Å, Crystal structure of the human RAD9-RAD1-HUS1-RAD17 complex
6HM5 2.33 Å, Crystal structure of TOPBP1 BRCT0,1,2 in complex with a RAD9 phosphopeptide
6J8Y 2.4 Å, Crystal structure of the human RAD9-HUS1-RAD1-RHINO complex
3A1J 2.5 Å, Crystal structure of the human Rad9-Hus1-Rad1 complex
8WU8 2.81 Å, Crystal structure of the human RAD9-RAD1(F64A/M256A/F266A)-HUS1-RHINO(88-99) complex
3G65 2.9 Å, Crystal Structure of the Human Rad9-Rad1-Hus1 DNA Damage Checkpoint Complex
3GGR 3.2 Å, Crystal Structure of the Human Rad9-Hus1-Rad1 complex

Browse structure collections

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