7VN4: MBP-fused BIL1/BZR1

Crystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with double-stranded DNA contaning TCCACGTGGA. Determined by X-ray diffraction at 2.1 Å resolution. Released 7 Dec 2022.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Serratia sp. (strain FS14), Arabidopsis thaliana, synthetic construct
Chains: 8
Atoms: 15,334
Mol. weight: 213.86 kDa
Released: 7 Dec 2022

Explore 7VN4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VN4 contains 105 α-helices and 103 β-strands across 4 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: 26 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	-342--338	5	20
α-helix	-331--317	15
β-strand	-314--310	5	20
α-helix	-305--297	9
β-strand	-289--285	5	20
α-helix	-284--282	3
α-helix	-281--276	6
β-strand	-272	1	21
α-helix	-271--269	3
α-helix	-265--262	4
β-strand	-259	1	22
α-helix	-257--252	6
β-strand	-250--249	2	23
β-strand	-246--245	2	23
β-strand	-242--237	6	20
β-strand	-234--230	5	24
β-strand	-220	1	25
α-helix	-216--208	9
β-strand	-203--201	3	24
α-helix	-194--187	8
β-strand	-181--176	6	26
β-strand	-173--166	8	26
α-helix	-162--148	15
α-helix	-138--130	9
β-strand	-126--121	6	24
α-helix	-119--117	3
α-helix	-116--111	6
β-strand	-106--103	4	24
α-helix	-102--100	3
β-strand	-99	1	25
β-strand	-98	1	27
β-strand	-95	1	27
α-helix	-91	1
β-strand	-90--89	2	28
β-strand	-88--82	7	20
β-strand	-81	1	21
α-helix	-75--69	7
α-helix	-68--64	5
α-helix	-61--52	10
β-strand	-47--46	2	20
β-strand	-44	1	22
α-helix	-43--37	7
α-helix	-33--22	12
β-strand	-20--19	2	28
α-helix	-18--17	2
α-helix	-12-3	16
α-helix	9-20	12
α-helix	23-26	4
α-helix	27-55	29
α-helix	65-75	11
β-strand	79-80	2	29
β-strand	86-87	2	29

Chain B: 27 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	-342--338	5	30
α-helix	-331--317	15
β-strand	-314--310	5	30
α-helix	-305--297	9
β-strand	-289--285	5	30
α-helix	-284--282	3
α-helix	-281--276	6
β-strand	-272	1	31
α-helix	-271--269	3
α-helix	-265--262	4
β-strand	-259	1	32
α-helix	-257--252	6
β-strand	-250--249	2	33
β-strand	-246--245	2	33
β-strand	-242--237	6	30
β-strand	-234--230	5	34
β-strand	-220	1	35
α-helix	-217--208	10
β-strand	-203--201	3	34
α-helix	-194--186	9
β-strand	-181--176	6	36
β-strand	-173--166	8	36
α-helix	-162--148	15
α-helix	-138--130	9
β-strand	-126--121	6	34
α-helix	-119--117	3
α-helix	-116--111	6
β-strand	-106--103	4	34
α-helix	-102--100	3
β-strand	-99	1	35
β-strand	-98	1	37
β-strand	-95	1	37
α-helix	-94--93	2
α-helix	-91	1
β-strand	-90--89	2	38
β-strand	-88--82	7	30
β-strand	-81	1	31
α-helix	-75--70	6
α-helix	-69--64	6
α-helix	-61--52	10
β-strand	-47--46	2	30
β-strand	-44	1	32
α-helix	-43--36	8
α-helix	-33--22	12
β-strand	-20--19	2	38
α-helix	-18--17	2
α-helix	-12-4	17
α-helix	9-20	12
α-helix	24-26	3
α-helix	27-55	29
α-helix	65-75	11
β-strand	79-80	2	39
β-strand	86-87	2	39

Chain C: 26 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	-342--338	5	1
α-helix	-331--317	15
β-strand	-314--310	5	1
α-helix	-305--297	9
β-strand	-289--285	5	1
α-helix	-284--282	3
α-helix	-281--276	6
β-strand	-272	1	2
α-helix	-271--269	3
α-helix	-265--262	4
β-strand	-259	1	3
α-helix	-257--252	6
β-strand	-250--249	2	4
β-strand	-246--245	2	4
β-strand	-242--237	6	1
β-strand	-234--230	5	5
β-strand	-220	1	6
α-helix	-216--207	10
β-strand	-203--201	3	5
α-helix	-194--185	10
β-strand	-181--176	6	7
β-strand	-173--166	8	7
α-helix	-162--148	15
α-helix	-138--130	9
β-strand	-126--121	6	5
α-helix	-119--117	3
α-helix	-116--111	6
β-strand	-106--103	4	5
α-helix	-102--100	3
β-strand	-99	1	6
β-strand	-98	1	8
β-strand	-95	1	8
α-helix	-91	1
β-strand	-90--89	2	9
β-strand	-88--82	7	1
β-strand	-81	1	2
α-helix	-75--69	7
α-helix	-68--64	5
α-helix	-61--52	10
β-strand	-47--46	2	1
β-strand	-44	1	3
α-helix	-43--37	7
α-helix	-33--22	12
β-strand	-20--19	2	9
α-helix	-18--17	2
α-helix	-12-3	16
α-helix	9-21	13
α-helix	22-26	5
α-helix	27-54	28
α-helix	65-75	11
β-strand	79-80	2	10
β-strand	86-87	2	10

Chain D: 26 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	-342--338	5	11
α-helix	-331--317	15
β-strand	-314--310	5	11
α-helix	-305--297	9
β-strand	-289--285	5	11
α-helix	-284--282	3
α-helix	-281--276	6
β-strand	-272	1	12
α-helix	-271--269	3
α-helix	-265--262	4
β-strand	-259	1	13
α-helix	-257--252	6
β-strand	-250--249	2	14
β-strand	-246--245	2	14
β-strand	-242--237	6	11
β-strand	-234--230	5	15
β-strand	-220	1	16
α-helix	-216--207	10
β-strand	-203--201	3	15
α-helix	-194--185	10
β-strand	-181--176	6	17
β-strand	-173--166	8	17
α-helix	-162--148	15
α-helix	-138--130	9
β-strand	-126--121	6	15
α-helix	-119--117	3
α-helix	-116--111	6
β-strand	-106--103	4	15
α-helix	-102--100	3
β-strand	-99--98	2	16
β-strand	-95--94	2	16
α-helix	-91	1
β-strand	-90--89	2	18
β-strand	-88--82	7	11
β-strand	-81	1	12
α-helix	-75--69	7
α-helix	-68--64	5
α-helix	-61--52	10
β-strand	-47--46	2	11
β-strand	-44	1	13
α-helix	-43--37	7
α-helix	-33--22	12
β-strand	-20--19	2	18
α-helix	-18--17	2
α-helix	-12-4	17
α-helix	9-21	13
α-helix	22-26	5
α-helix	27-54	28
α-helix	65-75	11
β-strand	79-80	2	19
β-strand	86-87	2	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1	A, B, C, D	protein	439	Serratia sp. (strain FS14), Arabidopsis thaliana	P0AEX9 (AlphaFold model), Q8S307 (AlphaFold model)
DNA (5'-d(tptptpcpcpapcpgptpgpapapapap*a)-3')	E, F, G, H	DNA	15	synthetic construct

Sequence of entity 1 (A, B, C, D), FASTA

>7VN4_1 Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1 (chains A, B, C, D)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSA
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDA
ALAAAQTNAARRKPSWRERENNRRRERRRRAVAAKIYTGLRAQGDYNLPKHCDNNEVLKA
LCVEAGWVVEEDGTTYRKG

Sequence of entity 2 (E, F, G, H), FASTA

>7VN4_2 DNA (5'-D(*TP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*AP*A)-3') (chains E, F, G, H)
TTTCCACGTGGAAAA

Primary citation

Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout. Nosaki, S., Mitsuda, N., Sakamoto, S. et al. Nat Plants (2022) 8:1440-1452. DOI 10.1038/s41477-022-01289-6 · PubMed

Other PDB entries of the same protein (UniProt P0AEX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C8F 1.15 Å, Crystal structure of the E. coli maltodextrin-binding protein
4EXK 1.28 Å, A chimera protein containing MBP fused to the C-terminal domain of the uncharacterized…
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
7KD4 1.31 Å, Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329…
5M13 1.37 Å, Synthetic nanobody in complex with MBP
5HZ7 1.43 Å, High-resolution crystal structure of the minor DNA-binding pilin ComP from Neisseria…
5H7Q 1.45 Å, Crystal structure of human MNDA PYD domain with MBP tag
6XDS 1.47 Å, Crystal structure of MBP-TREM2 Ig domain fusion with fragment,…
4IRL 1.47 Å, X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
9CLC 1.48 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan

Browse structure collections

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