7VDV: Histone H4
The overall structure of human chromatin remodeling PBAF-nucleosome complex. Determined by electron microscopy at 3.4 Å resolution. Released 18 May 2022.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organisms
- Xenopus laevis, synthetic construct, Homo sapiens
- Chains
- 24
- Atoms
- 40,028
- Mol. weight
- 1263.12 kDa
- Ligands
- BEF, MG, ADP
- Released
- 18 May 2022
Explore 7VDV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7VDV contains 228 α-helices and 108 β-strands across 21 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, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1594 | 1 | 32 |
| α-helix | 1597-1599 | 3 | |
| α-helix | 1602-1615 | 14 | |
| α-helix | 1627-1632 | 6 | |
| α-helix | 1643-1646 | 4 | |
| α-helix | 1650-1652 | 3 | |
| α-helix | 1663-1678 | 16 | |
Chain A: 42 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 175-192 | 18 | |
| α-helix | 198-203 | 6 | |
| α-helix | 363-386 | 24 | |
| α-helix | 395-422 | 28 | |
| α-helix | 430-432 | 3 | |
| β-strand | 445-446 | 2 | 11 |
| α-helix | 451-515 | 65 | |
| α-helix | 546-556 | 11 | |
| α-helix | 732-735 | 4 | |
| α-helix | 756-771 | 16 | |
| β-strand | 776-777 | 2 | 12 |
| α-helix | 785-798 | 14 | |
| β-strand | 807-810 | 4 | 12 |
| α-helix | 812-824 | 13 | |
| β-strand | 831-833 | 3 | 12 |
| α-helix | 838-842 | 5 | |
| α-helix | 845-850 | 6 | |
| β-strand | 855-859 | 5 | 12 |
| α-helix | 860-865 | 6 | |
| α-helix | 867-870 | 4 | |
| β-strand | 877-880 | 4 | 12 |
| α-helix | 883-886 | 4 | |
| α-helix | 892-900 | 9 | |
| β-strand | 905-909 | 5 | 12 |
| α-helix | 918-928 | 11 | |
| α-helix | 930-933 | 4 | |
| α-helix | 963-971 | 9 | |
| α-helix | 973-975 | 3 | |
| α-helix | 981-984 | 4 | |
| β-strand | 992-996 | 5 | 13 |
| α-helix | 1002-1013 | 12 | |
| β-strand | 1016-1018 | 3 | 14 |
| β-strand | 1032-1034 | 3 | 14 |
| α-helix | 1038-1047 | 10 | |
| α-helix | 1050-1052 | 3 | |
| α-helix | 1054-1062 | 9 | |
| α-helix | 1073-1078 | 6 | |
| α-helix | 1080-1095 | 16 | |
| β-strand | 1099-1103 | 5 | 13 |
| α-helix | 1106-1118 | 13 | |
| β-strand | 1123-1126 | 4 | 13 |
| α-helix | 1132-1143 | 12 | |
| β-strand | 1151-1155 | 5 | 13 |
| α-helix | 1156-1159 | 4 | |
| β-strand | 1170-1173 | 4 | 13 |
| α-helix | 1180-1187 | 8 | |
| α-helix | 1198-1199 | 2 | |
| β-strand | 1200-1204 | 5 | 13 |
| α-helix | 1210-1225 | 16 | |
| α-helix | 1226-1230 | 5 | |
| α-helix | 1242-1251 | 10 | |
| α-helix | 1252-1254 | 3 | |
| α-helix | 1268-1273 | 6 | |
| α-helix | 1277-1291 | 15 | |
| α-helix | 1294-1296 | 3 | |
| α-helix | 1307-1309 | 3 | |
| α-helix | 1311-1314 | 4 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 1 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 2 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 92-96 | 5 | |
| β-strand | 101-102 | 2 | 6 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 5 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-123 | 19 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-54 | 10 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 8 |
| α-helix | 121-131 | 11 | |
Chain F: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-20 | 3 | |
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 46 | 1 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 6 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 3 |
13 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 H4 | B, F | protein | 103 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 130 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | D, H | protein | 126 | Xenopus laevis | P02281 (AlphaFold model) |
| Histone H3 | E, K | protein | 136 | Xenopus laevis | P84233 (AlphaFold model) |
| DNA (207-mer) | I | DNA | 207 | synthetic construct | |
| DNA (207-mer) | J | DNA | 207 | synthetic construct | |
| Isoform 2 of Transcription activator BRG1 | A | protein | 1485 | Homo sapiens | P51532 |
| Actin-like protein 6A | N | protein | 429 | Homo sapiens | O96019 |
| Actin, cytoplasmic 1 | P | protein | 375 | Homo sapiens | P60709 |
| AT-rich interactive domain-containing protein 2,AT-rich interactive domain-containing protein 2 | Q | protein | 870 | Homo sapiens | Q68CP9 |
| PHD finger protein 10 | R | protein | 514 | Homo sapiens | Q8WUB8 |
| Isoform 2 of Bromodomain-containing protein 7 | T | protein | 652 | Homo sapiens | Q9NPI1 |
7 more molecules are not listed.
Sequence of entity 1 (B, F), FASTA
>7VDV_1 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 2 (C, G), FASTA
>7VDV_2 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK
Sequence of entity 3 (D, H), FASTA
>7VDV_3 Histone H2B 1.1 (chains D, H)
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 4 (E, K), FASTA
>7VDV_4 Histone H3 (chains E, K)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 5 (I), FASTA
>7VDV_5 DNA (207-MER) (chains I)
GGACCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAG
ACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGG
GGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGAAGCTTGTCGAGAA
GTACTAGAGGATCATAATCAGCCATAC
Sequence of entity 6 (J), FASTA
>7VDV_6 DNA (207-MER) (chains J)
GTATGGCTGATTATGATCCTCTAGTACTTCTCGACAAGCTTCAGGATGTATATATCTGAC
ACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTA
CGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGAT
TCTCCAGGGCGGCCGCGTATAGGGTCC
Sequence of entity 7 (A), FASTA
>7VDV_7 Isoform 2 of Transcription activator BRG1 (chains A)
MQALGQQNRGPTPFNQNQLHQLRAQIMAYKMLARGQPLPDHLQMAVQGKRPMPGMQQQMP
TLPPPSVSATGPGPGPGPGPGPGPGPAPPNYSRPHGMGGPNMPPPGPSGVPPGMPGQPPG
GPPKPWPEGPMANAAAPTSTPQKLIPPQPTGRPSPAPPAVPPAASPVMPPQTQSPGQPAQ
PAPMVPLHQKQSRITPIQKPRGLDPVEILQEREYRLQARIAHRIQELENLPGSLAGDLRT
KATIELKALRLLNFQRQLRQEVVVCMRRDTALETALNAKAYKRSKRQSLREARITEKLEK
QQKIEQERKRRQKHQEYLNSILQHAKDFKEYHRSVTGKIQKLTKAVATYHANTEREQKKE
NERIEKERMRRLMAEDEEGYRKLIDQKKDKRLAYLLQQTDEYVANLTELVRQHKAAQVAK
EKKKKKKKKKAENAEGQTPAIGPDGEPLDETSQMSDLPVKVIHVESGKILTGTDAPKAGQ
LEAWLEMNPGYEVAPRSDSEESGSEEEEEEEEEEQPQAAQPPTLPVEEKKKIPDPDSDDV
SEVDARHIIENAKQDVDDEYGVSQALARGLQSYYAVAHAVTERVDKQSALMVNGVLKQYQ
IKGLEWLVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRINGPFLIIVPLSTLSNW
AYEFDKWAPSVVKVSYKGSPAARRAFVPQLRSGKFNVLLTTYEYIIKDKHILAKIRWKYM
IVDEGHRMKNHHCKLTQVLNTHYVAPRRLLLTGTPLQNKLPELWALLNFLLPTIFKSCST
FEQWFNAPFAMTGEKVDLNEEETILIIRRLHKVLRPFLLRRLKKEVEAQLPEKVEYVIKC
DMSALQRVLYRHMQAKGVLLTDGSEKDKKGKGGTKTLMNTIMQLRKICNHPYMFQHIEES
FSEHLGFTGGIVQGLDLYRASGKFELLDRILPKLRATNHKVLLFCQMTSLMTIMEDYFAY
RGFKYLRLDGTTKAEDRGMLLKTFNEPGSEYFIFLLSTRAGGLGLNLQSADTVIIFDSDW
NPHQDLQAQDRAHRIGQQNEVRVLRLCTVNSVEEKILAAAKYKLNVDQKVIQAGMFDQKS
SSHERRAFLQAILEHEEQDEEEDEVPDDETVNQMIARHEEEFDLFMRMDLDRRREEARNP
KRKPRLMEEDELPSWIIKDDAEVERLTCEEEEEKMFGRGSRHRKEVDYSDSLTEKQWLKA
IEEGTLEEIEEEVRQKKSSRKRKRDSDAGSSTPTTSTRSRDKDDESKKQKKRGRPPAEKL
SPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIK
ERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDDSE
GEESEEEEEGEEEGSESESRSVKVKIKLGRKEKAQDRLKGGRRRPSRGSRAKPVVSDDDS
EEEQEEDRSGSGSEEDASGGSWSHPQFEKWSHPQFEKWSHPQFEK
Sequence of entity 8 (N), FASTA
>7VDV_8 Actin-like protein 6A (chains N)
MSGGVYGGDEVGALVFDIGSYTVRAGYAGEDCPKVDFPTAIGMVVERDDGSTLMEIDGDK
GKQGGPTYYIDTNALRVPRENMEAISPLKNGMVEDWDSFQAILDHTYKMHVKSEASLHPV
LMSEAPWNTRAKREKLTELMFEHYNIPAFFLCKTAVLTAFANGRSTGLILDSGATHTTAI
PVHDGYVLQQGIVKSPLAGDFITMQCRELFQEMNIELVPPYMIASKEAVREGSPANWKRK
EKLPQVTRSWHNYMCNCVIQDFQASVLQVSDSTYDEQVAAQMPTVHYEFPNGYNCDFGAE
RLKIPEGLFDPSNVKGLSGNTMLGVSHVVTTSVGMCDIDIRPGLYGSVIVAGGNTLIQSF
TDRLNRELSQKTPPSMRLKLIANNTTVERRFSSWIGGSILASLGTFQQMWISKQEYEEGG
KQCVERKCP
Sequence of entity 9 (P), FASTA
>7VDV_9 Actin, cytoplasmic 1 (chains P)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF
Sequence of entity 10 (Q), FASTA
>7VDV_10 AT-rich interactive domain-containing protein 2,AT-rich interactive domain-containing protein 2 (chains Q)
MANSTGKAPPDERRKGLAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGF
AKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYLRYLEKYEKVHHFGEDDDEVPPGNPKP
QLPIGAIPSSYNYQQHSVSDYLRQSYGLSMDFNSPNDYNKLVLSLLSGLPNEVDFAINVC
TLLSNESKHVMQLEKDPKIITLLLANAGVFDDTLGSFSTVFGEEWKEKTDRDFVKFWKDI
VDDNEVRDLISDRNKSHEGTSGEWIWESLFHPPRKLGINDIEGQRVLQIAVILRNLSFEE
GNVKLLAANRTCLRFLLLSAHSHFISLRQLGLDTLGNIAAELLLDPVDFKTTHLMFHTVT
KCLMSRDRFLKMRGMEILGNLCKAEDNGVLICEYVDQDSYREIICHLTLPDVLLVISTLE
VLYMLTEMGDVACTKIAKVEKSIDMLVCLVSMDIQMFGPDALAAVKLIEHPSSSHQMLSE
IRPQAIEQVQTQTHVASAPASRAVVAQHVAPPPGIVEIDSEKFACQWLNAHFEVNPDCSV
SRAEMYSEYLSTCSKLARGGILTSTGFYKCLRTVFPNHTVKRVEDSSSNGQAHIHVVGVK
RRAIPLPIQMYYQQQPVSTSVVRVDSNTPMPPSPAVQVQGQPNSSQPSPFSGSSQPGDPM
RKPGQNFMCLWQSCKKWFQTPSQVFYHAATEHGGKDVYPGQCLWEGCEPFQRQRFSFITH
LQDKHCSKDALLAGLKQDEPGQAGSQKSSTKQPTVGGTSSTPRAQKAIVNHPSAALMALR
RGSRNLVFRDFTDEKEGPITKHIRLTAALILKNIGKYSECGRRLLKRHENNLSVLAISNM
EASSTLAKCLYELNFTVQSKEQEKDSEMLQ
Sequence of entity 11 (R), FASTA
>7VDV_11 PHD finger protein 10 (chains R)
MHHHHHHHHHHHHGEFMAAAAGPGAALSPRPCDSDPATPGAQSPKDDNEDNSNDGTQPSK
RRRMGSGDSSRSCETSSQDLGFSYYPAENLIEYKWPPDETGEYYMLQEQVSEYLGVTSFK
RKYPDLERRDLSHKEKLYLRELNVITETQCTLGLTALRSDEVIDLMIKEYPAKHAEYSVI
LQEKERQRITDHYKEYSQMQQQNTQKVEASKVPEYIKKAAKKAAEFNSNLNRERMEERRA
YFDLQTHVIQVPQGKYKVLPTERTKVSSYPVALIPGQFQEYYKRYSPDELRYLPLNTALY
EPPLDPELPALDSDGDSDDGEDGRGDEKRKNKGTSDSSSGNVSEGESPPDSQEDSFQGRQ
KSKDKAATPRKDGPKRSVLSKSVPGYKPKVIPNAICGICLKGKESNKKGKAESLIHCSQC
ENSGHPSCLDMTMELVSMIKTYPWQCMECKTCIICGQPHHEEEMMFCDMCDRGYHTFCVG
LGAIPSGRWICDCCQRAPPTPRKVGRRGKNSKEG
Sequence of entity 12 (T), FASTA
>7VDV_12 Isoform 2 of Bromodomain-containing protein 7 (chains T)
MGKKHKKHKSDKHLYEEYVEKPLKLVLKVGGNEVTELSTGSSGHDSSLFEDKNDHDKHKD
RKRKKRKKGEKQIPGEEKGRKRRRVKEDKKKRDRDRVENEAEKDLQCHAPVRLDLPPEKP
LTSSLAKQEEVEQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFST
MKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERIQSL
KQSIDFMADLQKTRKQKDGTDTSQSGEDGGCWQREREDSGDAEAHAFKSPSKENKKKDKD
MLEDKFKSNNLEREQEQLDRIVKESGGKLTRRLVNSQCEFERRKPDGTTTLGLLHPVDPI
VGEPGYCPVRLGMTTGRLQSGVNTLQGFKEDKRNKVTPVLYLNYGPYSSYAPHYDSTFAN
ISKDDSDLIYSTYGEDSDLPSDFSIHEFLATCQDYPYVMADSLLDVLTKGGHSRTLQEME
MSLPEDEGHTRTLDTAKEMEQITEVEPPGRLDSSTQDRLIALKAVTNFGVPVEVFDSEEA
EIFQKKLDETTRLLRELQEAQNERLSTRPPPNMICLLGPSYREMHLAEQVTNNLKELAQQ
VTPGDIVSTYGVRKAMGISIPSPVMENNFVDLTEDTEEPKKTDVAECGPGGS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| BEF | Beryllium trifluoride ion | Be F3 | 1 |
| MG | Magnesium ion | Mg | 1 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
Primary citation
Structure of human chromatin-remodelling PBAF complex bound to a nucleosome. Yuan, J.J., Chen, K.J., Zhang, W.B. et al. Nature (2022) 605:166-171. DOI 10.1038/s41586-022-04658-5 · PubMed
Other PDB entries of the same protein (UniProt P62799 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
- 1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
- 1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
- 1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
- 3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
- 3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
- 3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
- 3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
- 6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
- 4ZBJ 2.25 Å, UBN1 peptide bound to H3.3/H4/Asf1
- 8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
- 1M19 2.3 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
Browse structure collections
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