9PGC: Helicase SRCAP

Trident submodule from human SRCAP-nucleosome complex in the fully-engaged state (focused refinement). Determined by electron microscopy at 3.8 Å resolution. Released 22 Jul 2026.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Homo sapiens, synthetic construct
Chains: 5
Atoms: 9,184
Mol. weight: 609.22 kDa
Ligands: AGS, MG
Released: 22 Jul 2026

Explore 9PGC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PGC contains 69 α-helices and 38 β-strands across 3 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: 36 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	179-251	73
α-helix	609-611	3
α-helix	617-619	3
α-helix	620-634	15
β-strand	639-641	3	1
α-helix	643-644	2
α-helix	649-659	11
α-helix	660-664	5
α-helix	669	1
β-strand	670-674	5	1
α-helix	676-678	3
α-helix	679-689	11
β-strand	695-697	3	1
α-helix	702-709	8
β-strand	720-724	5	1
α-helix	725-730	6
α-helix	732-737	6
β-strand	740-745	6	1
α-helix	748-751	4
α-helix	757-763	7
β-strand	767-773	7	1
α-helix	782-792	11
α-helix	800-803	4
α-helix	804-808	5
α-helix	809-816	8
α-helix	823-833	11
β-strand	837-838	2	1
α-helix	842-845	4
β-strand	852-859	8	2
α-helix	863-875	13
α-helix	890-902	13
α-helix	904-906	3
α-helix	909-911	3
β-strand	913	1	3
β-strand	2031	1	3
α-helix	2032-2034	3
α-helix	2036-2040	5
α-helix	2043-2058	16
β-strand	2062-2066	5	2
α-helix	2069-2082	14
β-strand	2086-2089	4	2
α-helix	2095-2107	13
β-strand	2113-2117	5	2
β-strand	2132-2135	4	2
α-helix	2142-2153	12
β-strand	2161-2168	8	2
α-helix	2172-2187	16
α-helix	2188-2192	5
α-helix	2198-2202	5
α-helix	2297-2308	12
α-helix	2311-2350	40

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	166-168	3
α-helix	169-201	33

Chain K: 31 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	12-13	2
β-strand	14-18	5	4
β-strand	22-27	6	4
β-strand	35-38	4	4
β-strand	41-44	4	5
α-helix	65-66	2
β-strand	67-69	3	5
α-helix	72-75	4
β-strand	83-85	3	5
β-strand	88-89	2	6
β-strand	92-93	2	6
α-helix	96-106	11
α-helix	107-111	5
α-helix	115-117	3
β-strand	120-124	5	4
α-helix	130-138	9
α-helix	139-143	5
β-strand	148-153	6	4
α-helix	154-161	8
β-strand	167-172	6	7
β-strand	177-183	7	7
β-strand	186-187	2	7
α-helix	189-191	3
β-strand	193-195	3	7
α-helix	199-213	15
α-helix	220-222	3
β-strand	223-227	5	8
α-helix	233-235	3
β-strand	236-239	4	8
α-helix	240	1
α-helix	248-265	18
β-strand	268	1	9
α-helix	276-280	5
α-helix	283-284	2
β-strand	285-288	4	10
β-strand	294-297	4	10
α-helix	300-306	7
α-helix	311-313	3
α-helix	319-321	3
α-helix	325-335	11
α-helix	338-340	3
α-helix	341-345	5
β-strand	348-351	4	7
α-helix	353-356	4
β-strand	358	1	9
α-helix	360-371	12
β-strand	380-381	2	7
α-helix	386-390	5
α-helix	392-402	11
α-helix	405-408	4
β-strand	411-412	2	4
α-helix	413-419	7
α-helix	420-422	3
α-helix	423-427	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Helicase SRCAP	A	protein	3230	Homo sapiens	Q6ZRS2
Vacuolar protein sorting-associated protein 72 homolog	B	protein	364	Homo sapiens	Q15906 (AlphaFold model)
Actin-like protein 6A	K	protein	429	Homo sapiens	O96019 (AlphaFold model)
DNA	Y	DNA	285	synthetic construct
DNA	Z	DNA	285	synthetic construct

Sequence of entity 1 (A), FASTA

>9PGC_1 Helicase SRCAP (chains A)
MQSSPSPAHPQLPVLQTQMVSDGMTGSNPVSPASSSSPASSGAGGISPQHIAQDSSLDGP
PGPPDGATVPLEGFSLSQAADLANKGPKWEKSHAEIAEQAKHEAEIETRIAELRKEGFWS
LKRLPKVPEPPRPKGHWDYLCEEMQWLSADFAQERRWKRGVARKVVRMVIRHHEEQRQKE
ERARREEQAKLRRIASTMAKDVRQFWSNVEKVVQFKQQSRLEEKRKKALDLHLDFIVGQT
EKYSDLLSQSLNQPLTSSKAGSSPCLGSSSAASSPPPPASRLDDEDGDFQPQEDEEEDDE
ETIEVEEQQEGNDAEAQRREIELLRREGELPLEELLRSLPPQLLEGPSSPSQTPSSHDSD
TRDGPEEGAEEEPPQVLEIKPPPSAVTQRNKQPWHPDEDDEEFTANEEEAEDEEDTIAAE
EQLEGEVDHAMELSELAREGELSMEELLQQYAGAYAPGSGSSEDEDEDEVDANSSDCEPE
GPVEAEEPPQEDSSSQSDSVEDRSEDEEDEHSEEEETSGSSASEESESEESEDAQSQSQA
DEEEEDDDFGVEYLLARDEEQSEADAGSGPPTPGPTTLGPKKEITDIAAAAESLQPKGYT
LATTQVKTPIPLLLRGQLREYQHIGLDWLVTMYEKKLNGILADEMGLGKTIQTISLLAHL
ACEKGNWGPHLIIVPTSVMLNWEMELKRWCPSFKILTYYGAQKERKLKRQGWTKPNAFHV
CITSYKLVLQDHQAFRRKNWRYLILDEAQNIKNFKSQRWQSLLNFNSQRRLLLTGTPLQN
SLMELWSLMHFLMPHVFQSHREFKEWFSNPLTGMIEGSQEYNEGLVKRLHKVLRPFLLRR
VKVDVEKQMPKKYEHVIRCRLSKRQRCLYDDFMAQTTTKETLATGHFMSVINILMQLRKV
CNHPNLFDPRPVTSPFITPGICFSTASLVLRATDVHPLQRIDMGRFDLIGLEGRVSRYEA
DTFLPRHRLSRRVLLEVATAPDPPPRPKPVKMKVNRMLQPVPKQEGRTVVVVNNPRAPLG
PVPVRPPPGPELSAQPTPGPVPQVLPASLMVSASPAGPPLIPASRPPGPVLLPPLQPNSG
SLPQVLPSPLGVLSGTSRPPTPTLSLKPTPPAPVRLSPAPPPGSSSLLKPLTVPPGYTFP
PAAATTTSTTTATATTTAVPAPTPAPQRLILSPDMQARLPSGEVVSIGQLASLAQRPVAN
AGGSKPLTFQIQGNKLTLTGAQVRQLAVGQPRPLQRNVVHLVSAGGQHHLISQPAHVALI
QAVAPTPGPTPVSVLPSSTPSTTPAPTGLSLPLAANQVPPTMVNNTGVVKIVVRQAPRDG
LTPVPPLAPAPRPPSSGLPAVLNPRPTLTPGRLPTPTLGTARAPMPTPTLVRPLLKLVHS
PSPEVSASAPGAAPLTISSPLHVPSSLPGPASSPMPIPNSSPLASPVSSTVSVPLSSSLP
ISVPTTLPAPASAPLTIPISAPLTVSASGPALLTSVTPPLAPVVPAAPGPPSLAPSGASP
SASALTLGLATAPSLSSSQTPGHPLLLAPTSSHVPGLNSTVAPACSPVLVPASALASPFP
SAPNPAPAQASLLAPASSASQALATPLAPMAAPQTAILAPSPAPPLAPLPVLAPSPGAAP
VLASSQTPVPVMAPSSTPGTSLASASPVPAPTPVLAPSSTQTMLPAPVPSPLPSPASTQT
LALAPALAPTLGGSSPSQTLSLGTGNPQGPFPTQTLSLTPASSLVPTPAQTLSLAPGPPL
GPTQTLSLAPAPPLAPASPVGPAPAHTLTLAPASSSASLLAPASVQTLTLSPAPVPTLGP
AAAQTLALAPASTQSPASQASSLVVSASGAAPLPVTMVSRLPVSKDEPDTLTLRSGPPSP
PSTATSFGGPRPRRQPPPPPRSPFYLDSLEEKRKRQRSERLERIFQLSEAHGALAPVYGT
EVLDFCTLPQPVASPIGPRSPGPSHPTFWTYTEAAHRAVLFPQQRLDQLSEIIERFIFVM
PPVEAPPPSLHACHPPPWLAPRQAAFQEQLASELWPRARPLHRIVCNMRTQFPDLRLIQY
DCGKLQTLAVLLRQLKAEGHRVLIFTQMTRMLDVLEQFLTYHGHLYLRLDGSTRVEQRQA
LMERFNADKRIFCFILSTRSGGVGVNLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRD
VHIYRLISERTVEENILKKANQKRMLGDMAIEGGNFTTAYFKQQTIRELFDMPLEEPSSS
SVPSAPEEEEETVASKQTHILEQALCRAEDEEDIRAATQAKAEQVAELAEFNENDGFPAG
EGEEAGRPGAEDEEMSRAEQEIAALVEQLTPIERYAMKFLEASLEEVSREELKQAEEQVE
AARKDLDQAKEEVFRLPQEEEEGPGAGDESSCGTGGGTHRRSKKAKAPERPGTRVSERLR
GARAETQGANHTPVISAHQTRSTTTPPRCSPARERVPRPAPRPRPTPASAPAAIPALVPV
PVSAPVPISAPNPITILPVHILPSPPPPSQIPPCSSPACTPPPACTPPPAHTPPPAQTCL
VTPSSPLLLGPPSVPISASVTNLPLGLRPEAELCAQALASPESLELASVASSETSSLSLV
PPKDLLPVAVEILPVSEKNLSLTPSAPSLTLEAGSIPNGQEQEAPDSAEGTTLTVLPEGE
ELPLCVSESNGLELPPSAASDEPLQEPLEADRTSEELTEAKTPTSSPEKPQELVTAEVAA
PSTSSSATSSPEGPSPARPPRRRTSADVEIRGQGTGRPGQPPGPKVLRKLPGRLVTVVEE
KELVRRRRQQRGAASTLVPGVSETSASPGSPSVRSMSGPESSPPIGGPCEAAPSSSLPTP
PQQPFIARRHIELGVTGGGSPENGDGALLAITPPAVKRRRGRPPKKNRSPADAGRGVDEA
PSSTLKGKTNGADPVPGPETLIVADPVLEPQLIPGPQPLGPQPVHRPNPLLSPVEKRRRG
RPPKARDLPIPGTISSAGDGNSESRTQPPPHPSPLTPLPPLLVCPTATVANTVTTVTIST
SPPKRKRGRPPKNPPSPRPSQLPVLDRDSTSVLESCGLGRRRQPQGQGESEGSSSDEDGS
RPLTRLARLRLEAEGMRGRKSGGSMVVAVIQDDLDLADSGPGGLELTPPVVSLTPKLRST
RLRPGSLVPPLETEKLPRKRAGAPVGGSPGLAKRGRLQPPSPLGPEGSVEESEAEASGEE
EEGDGTPRRRPGPRRLVGTTNQGDQRILRSSAPPSLAGPAVSHRGRKAKT

Sequence of entity 2 (B), FASTA

>9PGC_2 Vacuolar protein sorting-associated protein 72 homolog (chains B)
MSLAGGRAPRKTAGNRLSGLLEAEEEDEFYQTTYGGFTEESGDDEYQGDQSDTEDEVDSD
FDIDEGDEPSSDGEAEEPRRKRRVVTKAYKEPLKSLRPRKVNTPAGSSQKAREEKALLPL
ELQDDGSDSRKSMRQSTAEHTRQTFLRVQERQGQSRRRKGPHCERPLTQEELLREAKITE
ELNLRSLETYERLEADKKKQVHKKRKCPGPIITYHSVTVPLVGEPGPKEENVDIEGLDPA
PSVSALTPHAGTGPVNPPARCSRTFITFSDDATFEEWFPQGRPPKVPVREVCPVTHRPAL
YRDPVTDIPYATARAFKIIREAYKKYITAHGLPPTASALGPGPPPPEPLPGSGPRALRQK
IVIK

Sequence of entity 3 (K), FASTA

>9PGC_3 Actin-like protein 6A (chains K)
MSGGVYGGDEVGALVFDIGSYTVRAGYAGEDCPKVDFPTAIGMVVERDDGSTLMEIDGDK
GKQGGPTYYIDTNALRVPRENMEAISPLKNGMVEDWDSFQAILDHTYKMHVKSEASLHPV
LMSEAPWNTRAKREKLTELMFEHYNIPAFFLCKTAVLTAFANGRSTGLILDSGATHTTAI
PVHDGYVLQQGIVKSPLAGDFITMQCRELFQEMNIELVPPYMIASKEAVREGSPANWKRK
EKLPQVTRSWHNYMCNCVIQDFQASVLQVSDSTYDEQVAAQMPTVHYEFPNGYNCDFGAE
RLKIPEGLFDPSNVKGLSGNTMLGVSHVVTTSVGMCDIDIRPGLYGSVIVAGGNTLIQSF
TDRLNRELSQKTPPSMRLKLIANNTTVERRFSSWIGGSILASLGTFQQMWISKQEYEEGG
KQCVERKCP

Sequence of entity 4 (Y), FASTA

>9PGC_4 DNA (chains Y)
ATCGAAGGGCGCCTATATAAGGGGGTGGGGGCGCGTTCGTCCTCCCTCTCCTCGCGGCGC
GAGTTTCAGGCAGCGCTGCGTCCTGCTGCGCACGTGGGAAGCCCTGCTGGAGAATCCCGG
TGCGCAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCAGCTACGCGC
TGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCAGCTGTCAGAT
ATGTACATCCTGTGATCCCCGGGTACCGAGCTCGAATTCACTGGC

Sequence of entity 5 (Z), FASTA

>9PGC_5 DNA (chains Z)
GCCAGTGAATTCGAGCTCGGTACCCGGGGATCACAGGATGTACATATCTGACAGCTGCCT
GGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTAGCTGCGTT
TAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTGCGCACCGGGATTCTCCAGC
AGGGCTTCCCACGTGCGCAGCAGGACGCAGCGCTGCCTGAAACTCGCGCCGCGAGGAGAG
GGAGGACGAACGCGCCCCCACCCCCTTATATAGGCGCCCTTCGAT

Ligands and cofactors

ID	Name	Formula	Copies
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	2
MG	Magnesium ion	Mg	2

Primary citation

Structural mechanism of histone H2A.Z exchange by human SRCAP-CFDP1 holoenzyme. Park, G., Wu, C., Louder, R.K. Sci Adv (2026) 12:eaei7728-eaei7728. DOI 10.1126/sciadv.aei7728 · PubMed

Other PDB entries of the same protein (UniProt Q6ZRS2), best resolution first:

9UBD 2.53 Å, The Structural Basis of the Recognition of the Histone Variant H2A.Z by the SRCAP…
8X15 3.2 Å, Structure of nucleosome-bound SRCAP-C in the apo state
8X19 3.2 Å, Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
8X1C 3.2 Å, Structure of nucleosome-bound SRCAP-C in the ADP-bound state
9NFX 3.3 Å, Human SRCAP-CFDP1-hexasome complex in the evicted state of the H2A.Z histone exchange…
9CA7 3.35 Å, Cryo-EM structure of human SRCAP-nucleosome complex in the fully-engaged state…
9NFY 3.4 Å, Human SRCAP-CFDP1-prenucleosome complex in the pre-inserted state of the H2A.Z histone…
9CA9 3.56 Å, Cryo-EM structure of the human SRCAP complex in the unbound state (composite structure)
9NFV 3.8 Å, Human SRCAP-CFDP1-nucleosome complex in the poised state of the H2A.Z histone exchange…
9NFW 3.8 Å, Human SRCAP-CFDP1-nucleosome complex in the activated state of the H2A.Z histone…
9NFZ 3.8 Å, Human SRCAP-nucleosome complex in the fully inserted state of the H2A.Z histone exchange…
9NG0 3.9 Å, Human SRCAP-nucleosome complex in the pre-dissociation state of the H2A.Z histone…

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