4O3M: Ternary complex of Bloom's syndrome helicase

Ternary complex of Bloom's syndrome helicase. Determined by X-ray diffraction at 2.3 Å resolution. Released 12 Mar 2014.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,427
Mol. weight: 88.21 kDa
Ligands: CA, ZN, ADP
Released: 12 Mar 2014

Explore 4O3M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4O3M contains 30 α-helices and 18 β-strands across 1 chain. 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: 30 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	643-645	3
α-helix	652-661	10
α-helix	672-680	9
β-strand	685-688	4	1
α-helix	697-705	9
β-strand	709-713	5	1
α-helix	717-729	13
β-strand	734-737	4	1
α-helix	743-753	11
β-strand	762-765	4	1
α-helix	769-772	4
α-helix	774-785	12
β-strand	789-794	6	1
α-helix	811-820	10
β-strand	826-830	5	1
α-helix	835-845	11
β-strand	851-853	3	1
β-strand	862-868	7	2
α-helix	871-873	3
α-helix	874-885	12
β-strand	891-894	4	2
α-helix	898-910	13
β-strand	915-918	4	2
α-helix	924-935	12
β-strand	942-945	4	2
β-strand	960-963	4	2
α-helix	970-977	8
β-strand	987-993	7	2
α-helix	995-1005	11
α-helix	1015-1031	17
α-helix	1037-1044	8
α-helix	1054-1057	4
α-helix	1059-1061	3
α-helix	1064-1067	4
β-strand	1075-1076	2	3
α-helix	1078-1090	13
β-strand	1110	1	4
α-helix	1111-1119	9
α-helix	1139-1151	13
β-strand	1155-1161	7	4
β-strand	1167-1173	7	4
α-helix	1177-1181	5
β-strand	1188-1189	2	3
α-helix	1210-1233	24
α-helix	1237-1239	3
α-helix	1243-1252	10
α-helix	1257-1260	4
α-helix	1268-1283	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bloom syndrome protein	A	protein	659	Homo sapiens	P54132 (AlphaFold model)
5'-d(apgpcpgptpcpgpapgpaptpcpcpapapg)-3'	P	DNA	16
5'-d(cptptpgpgpaptpcptpcpgpapcpgpcptpcptpcpcpcptptpa)-3'	T	DNA	24

Sequence of entity 1 (A), FASTA

>4O3M_1 Bloom syndrome protein (chains A)
KHERFQSLSFPHTKEMMKIFHKKFGLHNFRTNQLEAINAALLGEDCFILMPTGGGKSLCY
QLPACVSPGVTVVISPLRSLIVDQVQKLTSLDIPATYLTGDKTDSEATNIYLQLSKKDPI
IKLLYVTPEKICASNRLISTLENLYERKLLARFVIDEAHCVSQWGHDFRQDYKRMNMLRQ
KFPSVPVMALTATANPRVQKDILTQLKILRPQVFSMSFNRHNLKYYVLPKKPKKVAFDCL
EWIRKHHPYDSGIIYCLSRRECDTMADTLQRDGLAALAYHAGLSDSARDEVQQKWINQDG
CQVICATIAFGMGIDKPDVRFVIHASLPKSVEGYYQESGRAGRDGEISHCLLFYTYHDVT
RLKRLIMMEKDGNHHTRETHFNNLYSMVHYCENITECRRIQLLAYFGENGFNPDFCKKHP
DVSCDNCCKTKDYKTRDVTDDVKSIVRFVQEHSSSQGMRNIKHVGPSGRFTMNMLVDIFL
GSKSAKIQSGIFGKGSAYSRHNAERLFKKLILDKILDEDLYINANDQAIAYVMLGNKAQT
VLNGNLKVDFMETENSSSVKKQKALVAKVSQREEMVKKCLGELTEVCKSLGKVFGVHYFN
IFNTVTLKKLAESLSSDPEVLLQIDGVTEDKLEKYGAEVISVLQKYSEWTSPAEDSSPG

Sequence of entity 2 (P), FASTA

>4O3M_2 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*AP*AP*G)-3' (chains P)
AGCGTCGAGATCCAAG

Sequence of entity 3 (T), FASTA

>4O3M_3 5'-D(*CP*TP*TP*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*CP*TP*TP*A)-3' (chains T)
CTTGGATCTCGACGCTCTCCCTTA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
ZN	Zinc ion	Zn	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structure of human Bloom's syndrome helicase in complex with ADP and duplex DNA. Swan, M.K., Legris, V., Tanner, A. et al. Acta Crystallogr D Biol Crystallogr (2014) 70:1465-1475. DOI 10.1107/S139900471400501X · PubMed

Other PDB entries of the same protein (UniProt P54132 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7XV0 1.5 Å, Crystal structure of RPA70N-BLMp1 fusion
7AUC 1.53 Å, Crystal structure of an engineered helicase domain construct for human Bloom syndrome…
7XUW 1.8 Å, Crystal structure of RPA70N-BLMp2 fusion
9P3E 2.0 Å, LC3B bound to BLM peptide
5LUP 2.03 Å, Structures of DHBN domain of human BLM helicase
5MK5 2.16 Å, Structures of DHBN domain of human BLM helicase
5U6K 2.6 Å, Crystal structure of TopBP1 BRCT4/5 in complex with a BLM phosphopeptide
3WE2 2.7 Å, Structure of BLM RQC domain bound to a phosphate ion
4CDG 2.79 Å, Crystal structure of the Bloom's syndrome helicase BLM in complex with Nanobody
3WE3 2.9 Å, Structure of BLM RQC domain bound to an arsenate ion
7AUD 2.96 Å, Structure of an engineered helicase domain construct for human Bloom syndrome protein…
4CGZ 3.2 Å, Crystal structure of the Bloom's syndrome helicase BLM in complex with DNA

Browse structure collections

About this viewer

MolViewer shows 4O3M 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.