7BDK: Human Brr2 Helicase Region

Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and ADP. Determined by X-ray diffraction at 2.52 Å resolution. Released 9 Jun 2021.

Method: X-ray diffraction
Resolution: 2.52 Å
Organism: Homo sapiens
Chains: 2
Atoms: 16,249
Mol. weight: 230.7 kDa
Ligands: ADP, MG
Released: 9 Jun 2021

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

Secondary structure: helices and β-sheets

7BDK contains 117 α-helices and 87 β-strands across 2 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 B: 105 helices, 71 β-strands

Element	Residues	Length	Sheet
α-helix	411-414	4
α-helix	419-421	3
α-helix	429-431	3
β-strand	435-438	4	1
β-strand	442-447	6	1
α-helix	448-454	7
α-helix	460-462	3
β-strand	463	1	2
α-helix	464-466	3
α-helix	469-471	3
β-strand	480	1	2
α-helix	483-493	11
β-strand	499-502	4	3
α-helix	509-522	14
β-strand	525	1	4
β-strand	531	1	4
α-helix	533-535	3
β-strand	537-541	5	3
α-helix	545-558	14
α-helix	560-562	3
β-strand	566-568	3	3
α-helix	569-570	2
α-helix	578-582	5
β-strand	585-588	4	3
α-helix	590-599	10
α-helix	606-608	3
β-strand	609-614	6	3
α-helix	617-621	5
α-helix	625-642	18
β-strand	647-652	6	3
α-helix	658-664	7
α-helix	669-672	4
β-strand	673-675	3	3
α-helix	678-680	3
β-strand	685-692	8	1
α-helix	697-715	19
β-strand	721-724	4	1
α-helix	730-744	15
α-helix	757-768	12
α-helix	774-776	3
β-strand	782-785	4	1
α-helix	791-802	12
β-strand	808-811	4	1
α-helix	813-818	6
β-strand	823	1	5
β-strand	825-828	4	1
β-strand	832-835	4	6
β-strand	840-843	4	6
α-helix	844-845	2
α-helix	846-854	9
β-strand	856	1	5
β-strand	865-872	8	1
α-helix	873-875	3
α-helix	876-882	7
α-helix	897-906	10
β-strand	912	1	7
α-helix	913-920	8
α-helix	924-931	8
α-helix	933-936	4
α-helix	950-966	17
β-strand	970-972	3	8
β-strand	978	1	7
β-strand	979-981	3	8
α-helix	983-990	8
α-helix	995-1004	10
α-helix	1011-1019	9
α-helix	1022-1024	3
α-helix	1034-1041	8
α-helix	1055-1067	13
α-helix	1075-1101	27
β-strand	1104	1	9
α-helix	1105-1120	16
α-helix	1128-1131	4
α-helix	1137-1139	3
α-helix	1140-1145	6
α-helix	1150-1153	4
α-helix	1160-1165	6
α-helix	1171-1180	10
β-strand	1184-1192	9	10
β-strand	1197-1206	10	10
α-helix	1212-1215	4
β-strand	1218-1226	9	11
β-strand	1232	1	9
β-strand	1233-1242	10	11
α-helix	1243-1245	3
β-strand	1250-1257	8	10
β-strand	1265-1272	8	11
β-strand	1279-1285	7	11
α-helix	1291-1302	12
α-helix	1304-1307	4
β-strand	1308	1	12
α-helix	1309-1312	4
α-helix	1315-1318	4
β-strand	1327	1	12
α-helix	1330-1334	5
α-helix	1336-1340	5
β-strand	1346-1349	4	13
α-helix	1356-1370	15
β-strand	1376-1379	4	13
α-helix	1383-1394	12
α-helix	1395-1400	6
β-strand	1405-1407	3	13
α-helix	1412-1414	3
α-helix	1416-1419	4
β-strand	1424-1427	4	13
α-helix	1429-1437	9
α-helix	1443-1446	4
β-strand	1450-1453	4	13
α-helix	1456-1460	5
α-helix	1464-1479	16
α-helix	1484-1485	2
β-strand	1486-1491	6	13
β-strand	1494	1	14
α-helix	1497-1503	7
α-helix	1508-1510	3
β-strand	1511-1513	3	13
α-helix	1516-1518	3
β-strand	1523-1530	8	15
α-helix	1535-1541	7
α-helix	1543-1553	11
β-strand	1559-1563	5	15
α-helix	1566-1582	17
β-strand	1590	1	16
α-helix	1594-1596	3
α-helix	1598-1601	4
α-helix	1607-1613	7
β-strand	1617-1620	4	15
α-helix	1626-1637	12
β-strand	1641	1	16
β-strand	1643-1647	5	15
α-helix	1648-1650	3
β-strand	1658	1	17
β-strand	1660-1664	5	15
β-strand	1667-1670	4	18
β-strand	1675-1678	4	18
α-helix	1679-1680	2
α-helix	1681-1688	8
β-strand	1691	1	17
β-strand	1700-1707	8	15
α-helix	1708-1710	3
α-helix	1711-1718	8
α-helix	1721	1
β-strand	1722	1	14
α-helix	1723	1
α-helix	1728-1730	3
α-helix	1733-1741	9
β-strand	1747	1	19
α-helix	1748-1755	8
α-helix	1759-1766	8
α-helix	1768-1771	4
α-helix	1780-1798	19
β-strand	1802-1805	4	19
β-strand	1809-1812	4	19
α-helix	1814-1821	8
α-helix	1826-1833	8
α-helix	1842-1850	9
α-helix	1853-1855	3
α-helix	1862-1864	3
α-helix	1865-1874	10
α-helix	1887-1899	13
α-helix	1906-1932	27
β-strand	1935	1	20
α-helix	1936-1951	16
α-helix	1959-1962	4
α-helix	1972-1975	4
α-helix	1982-1986	5
α-helix	1990-1996	7
α-helix	2003-2013	11
β-strand	2017-2023	7	21
β-strand	2034-2043	10	21
β-strand	2063-2070	8	20
β-strand	2075-2083	9	20
β-strand	2085	1	21
β-strand	2087-2095	9	21
β-strand	2100-2110	11	20
β-strand	2118-2126	9	20

Chain J: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	2072-2080	9
α-helix	2083-2088	6
β-strand	2090-2092	3	22
β-strand	2103-2107	5	22
α-helix	2108-2116	9
β-strand	2125-2131	7	22
β-strand	2139-2146	8	22
β-strand	2150	1	23
β-strand	2151-2152	2	24
β-strand	2157-2158	2	24
α-helix	2163-2164	2
α-helix	2168-2171	4
β-strand	2173-2181	9	22
α-helix	2190-2202	13
β-strand	2212-2217	6	22
β-strand	2223-2230	8	22
α-helix	2232-2238	7
α-helix	2253-2255	3
β-strand	2256-2258	3	22
α-helix	2259	1
β-strand	2260-2264	5	22
β-strand	2270-2272	3	22
β-strand	2273-2274	2	25
β-strand	2280	1	23
β-strand	2296-2297	2	25
α-helix	2300-2303	4
α-helix	2307-2309	3
α-helix	2311-2315	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
U5 small nuclear ribonucleoprotein 200 kDa helicase	B	protein	1747	Homo sapiens	O75643 (AlphaFold model)
Pre-mRNA-processing-splicing factor 8	J	protein	263	Homo sapiens	Q6P2Q9 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>7BDK_1 U5 small nuclear ribonucleoprotein 200 kDa helicase (chains B)
GAEFMDLDQGGEALAPRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPA
LKPKPFGSEEQLLPVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLCAPTGAGK
TNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAEL
TGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDDRGPVLE
ALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTY
VGITEKKAIKRFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLG
LFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVL
VSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGIL
ITSHGELQYYLSLLNQQLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLYIRM
LRSPTLYGISHDDLKGDPLLDQRRLDLVHTAALMLDKNNLVKYDKKTGNFQVTELGRIAS
HYYITNDTVQTYNQLLKPTLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVK
ESIEEPSAKINVLLQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNRGWAQLTD
KTLNLCKMIDKRMWQSMCPLRQFRKLPEEVVKKIEKKNFPFERLYDLNHNEIGELIRMPK
MGKTIHKYVHLFPKLELSVHLQPITRSTLKVELTITPDFQWDEKVHGSSEAFWILVEDVD
SEVILHHEYFLLKAKYAQDEHLITFFVPVFEPLPPQYFIRVVSDRWLSCETQLPVSFRHL
ILPEKYPPPTELLDLQPLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVG
APTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLT
GETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVLEV
ICSRMRYISSQIERPIRIVALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQG
FNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRF
LHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRS
LCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGS
KKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYRRMTQNPN
YYNLQGISHRHLSDHLSELVEQTLSDLEQSKCISIEDEMDVAPLNLGMIAAYYYINYTTI
ELFSMSLNAKTKVRGLIEIISNAAEYENIPIRHHEDNLLRQLAQKVPHKLNNPKFNDPHV
KTNLLLQAHLSRMQLSAELQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMV
TQAMWSKDSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEERNALLQLTDSQIADVAR
FCNRYPNIELSYEVVDKDSIRSGGPVVVLVQLEREEEVTGPVIAPLFPQKREEGWWVVIG
DAKSNSLISIKRLTLQQKAKVKLDFVAPATGAHNYTLYFMSDAYMGCDQEYKFSVDVKEA
ETDSDSD

Sequence of entity 2 (J), FASTA

>7BDK_2 Pre-mRNA-processing-splicing factor 8 (chains J)
GPLGSMTQTFSSKTEWRVRAISAANLHLRTNHIYVSSDDIKETGYTYILPKNVLKKFICI
SDLRAQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGTHQTVHLPGQLPQHEYLKEMEPLGW
IHTQPNESPQLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTPGSCTLTAYKLTPSGYEW
GRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGFFMVPAQSSWNYNFMGVRHDPNMKYELQ
LANPKEFYHEVHRPSHFLNFALL

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	2

Primary citation

Long-range allostery mediates cooperative adenine nucleotide binding by the Ski2-like RNA helicase Brr2. Absmeier, E., Vester, K., Ghane, T. et al. J Biol Chem (2021) 297:100829-100829. DOI 10.1016/j.jbc.2021.100829 · PubMed

Other PDB entries of the same protein (UniProt O75643 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2Q0Z 2.0 Å, Crystal structure of Q9P172/Sec63 from Homo sapiens. Northeast Structural Genomics…
8BCE 2.05 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 76
8BC9 2.3 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 24
8BCC 2.35 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 39
8BCB 2.38 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 34
8BC8 2.39 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 18
8BCG 2.39 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 86
6S8Q 2.39 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1
9S2E 2.4 Å, Human intron-lariat spliceosome-Aquarius (ILSaqr)
8BCF 2.42 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 78
7BDJ 2.59 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and mant-ATPgammaS
6S9I 2.6 Å, Human Brr2 Helicase Region D534C/N1866C in complex with C-tail deleted Jab1

Browse structure collections

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