8X1C: Nucleosome-bound SRCAP-C in the ADP-bound state
Structure of nucleosome-bound SRCAP-C in the ADP-bound state. Determined by electron microscopy at 3.2 Å resolution. Released 6 Mar 2024.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 25
- Atoms
- 56,519
- Mol. weight
- 1168.33 kDa
- Ligands
- ATP, ADP
- Released
- 6 Mar 2024
Explore 8X1C in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8X1C contains 333 α-helices and 292 β-strands across 23 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, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 1 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 2 |
| α-helix | 112-115 | 4 | |
Chain B: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 1 |
| α-helix | 53-80 | 28 | |
| α-helix | 88-98 | 11 | |
| α-helix | 101-103 | 3 | |
| α-helix | 104-119 | 16 | |
Chain C: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-56 | 11 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 3 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 4 |
| α-helix | 121-131 | 11 | |
Chain D: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 4 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 3 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 2 |
Chain E: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-34 | 8 | |
| β-strand | 43 | 1 | 5 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 6 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 7 |
Chain F: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 6 |
| α-helix | 53-80 | 28 | |
| β-strand | 86 | 1 | 5 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
Chain G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 8 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 9 |
| α-helix | 121-130 | 10 | |
Chain H: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 46 | 1 | 9 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 8 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 7 |
15 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H2A type 1-C | A, E | protein | 130 | Homo sapiens | Q93077 (AlphaFold model) |
| Histone H2B type 1-C/E/F/G/I | B, F | protein | 126 | Homo sapiens | P62807 (AlphaFold model) |
| Histone H3.1 | C, G | protein | 136 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | D, H | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Helicase SRCAP | I | protein | 3230 | Homo sapiens | Q6ZRS2 |
| Vacuolar protein sorting-associated protein 72 homolog | J | protein | 364 | Homo sapiens | Q15906 |
| Actin-related protein 6 | K | protein | 396 | Homo sapiens | Q9GZN1 |
| Zinc finger HIT domain-containing protein 1 | L | protein | 154 | Homo sapiens | O43257 |
| RuvB-like 1 | M, O, Q | protein | 456 | Homo sapiens | Q9Y265 |
| RuvB-like 2 | N, P, R | protein | 463 | Homo sapiens | Q9Y230 |
| Actin, cytoplasmic 1 | S, U | protein | 375 | Homo sapiens | P60709 |
| Actin-like protein 6A | T | protein | 429 | Homo sapiens | O96019 |
4 more molecules are not listed.
Sequence of entity 1 (A, E), FASTA
>8X1C_1 Histone H2A type 1-C (chains A, E)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 2 (B, F), FASTA
>8X1C_2 Histone H2B type 1-C/E/F/G/I (chains B, F)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK
Sequence of entity 3 (C, G), FASTA
>8X1C_3 Histone H3.1 (chains C, G)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 4 (D, H), FASTA
>8X1C_4 Histone H4 (chains D, H)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 5 (I), FASTA
>8X1C_5 Helicase SRCAP (chains I)
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 6 (J), FASTA
>8X1C_6 Vacuolar protein sorting-associated protein 72 homolog (chains J)
MSLAGGRAPRKTAGNRLSGLLEAEEEDEFYQTTYGGFTEESGDDEYQGDQSDTEDEVDSD
FDIDEGDEPSSDGEAEEPRRKRRVVTKAYKEPLKSLRPRKVNTPAGSSQKAREEKALLPL
ELQDDGSDSRKSMRQSTAEHTRQTFLRVQERQGQSRRRKGPHCERPLTQEELLREAKITE
ELNLRSLETYERLEADKKKQVHKKRKCPGPIITYHSVTVPLVGEPGPKEENVDIEGLDPA
PSVSALTPHAGTGPVNPPARCSRTFITFSDDATFEEWFPQGRPPKVPVREVCPVTHRPAL
YRDPVTDIPYATARAFKIIREAYKKYITAHGLPPTASALGPGPPPPEPLPGSGPRALRQK
IVIK
Sequence of entity 7 (K), FASTA
>8X1C_7 Actin-related protein 6 (chains K)
MTTLVLDNGAYNAKIGYSHENVSVIPNCQFRSKTARLKTFTANQIDEIKDPSGLFYILPF
QKGYLVNWDVQRQVWDYLFGKEMYQVDFLDTNIIITEPYFNFTSIQESMNEILFEEYQFQ
AVLRVNAGALSAHRYFRDNPSELCCIIVDSGYSFTHIVPYCRSKKKKEAIIRINVGGKLL
TNHLKEIISYRQLHVMDETHVINQVKEDVCYVSQDFYRDMDIAKLKGEENTVMIDYVLPD
FSTIKKGFCKPREEMVLSGKYKSGEQILRLANERFAVPEILFNPSDIGIQEMGIPEAIVY
SIQNLPEEMQPHFFKNIVLTGGNSLFPGFRDRVYSEVRCLTPTDYDVSVVLPENPITYAW
EGGKLISENDDFEDMVVTREDYEENGHSVCEEKFDI
Sequence of entity 8 (L), FASTA
>8X1C_8 Zinc finger HIT domain-containing protein 1 (chains L)
MVEKKTSVRSQDPGQRRVLDRAARQRRINRQLEALENDNFQDDPHAGLPQLGKRLPQFDD
DADTGKKKKKTRGDHFKLRFRKNFQALLEEQNLSVAEGPNYLTACAGPPSRPQRPFCAVC
GFPSPYTCVSCGARYCTVRCLGTHQETRCLKWTV
Sequence of entity 9 (M, O, Q), FASTA
>8X1C_9 RuvB-like 1 (chains M, O, Q)
MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKK
MAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAI
GLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESL
QKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTL
HDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLF
VDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMI
IRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKIN
GKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK
Sequence of entity 10 (N, P, R), FASTA
>8X1C_10 RuvB-like 2 (chains N, P, R)
MATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVL
EMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALT
QAFRRSIGVRIKEETEIIEGEVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIE
SLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAMGSQTKFVQCPDGELQKRKEVVH
TVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDE
VHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTT
PYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTE
VQVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNELKGETMDTS
Sequence of entity 11 (S, U), FASTA
>8X1C_11 Actin, cytoplasmic 1 (chains S, U)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF
Sequence of entity 12 (T), FASTA
>8X1C_12 Actin-like protein 6A (chains T)
MSGGVYGGDEVGALVFDIGSYTVRAGYAGEDCPKVDFPTAIGMVVERDDGSTLMEIDGDK
GKQGGPTYYIDTNALRVPRENMEAISPLKNGMVEDWDSFQAILDHTYKMHVKSEASLHPV
LMSEAPWNTRAKREKLTELMFEHYNIPAFFLCKTAVLTAFANGRSTGLILDSGATHTTAI
PVHDGYVLQQGIVKSPLAGDFITMQCRELFQEMNIELVPPYMIASKEAVREGSPANWKRK
EKLPQVTRSWHNYMCNCVIQDFQASVLQVSDSTYDEQVAAQMPTVHYEFPNGYNCDFGAE
RLKIPEGLFDPSNVKGLSGNTMLGVSHVVTTSVGMCDIDIRPGLYGSVIVAGGNTLIQSF
TDRLNRELSQKTPPSMRLKLIANNTTVERRFSSWIGGSILASLGTFQQMWISKQEYEEGG
KQCVERKCP
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 3 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 7 |
Primary citation
Structural insights into histone exchange by human SRCAP complex. Yu, J., Sui, F., Gu, F. et al. Cell Discov (2024) 10:15-15. DOI 10.1038/s41421-023-00640-1 · PubMed
Other PDB entries of the same protein (UniProt Q93077 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7R5R 2.44 Å, Structure of the human CCAN CENP-A alpha-satellite complex
- 8OX0 2.52 Å, Structure of apo telomeric nucleosome
- 7PII 2.68 Å, Structure of the human CCAN CENP-A alpha-satellite complex
- 7U46 2.68 Å, Cryo-EM structure of CENP-A nucleosome (palindromic alpha satellite DNA) in complex with…
- 8OOP 2.7 Å, CryoEM Structure INO80core Hexasome complex composite model state2
- 8OX1 2.7 Å, Structure of TRF1core in complex with telomeric nucleosome
- 8OO7 2.8 Å, CryoEM Structure INO80core Hexasome complex composite model state1
- 9EOZ 3.1 Å, Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0
- 7A08 3.11 Å, CryoEM Structure of cGAS Nucleosome complex
- 8OOA 3.18 Å, CryoEM Structure INO80core Hexasome complex Hexasome refinement state1
- 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
Browse structure collections
About this viewer
MolViewer shows 8X1C directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.