7VN3: MBP-fused BIL1/BZR1

Crystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with double-stranded DNA contaning CACACGTGTG. Determined by X-ray diffraction at 1.94 Å resolution. Released 7 Dec 2022.

Method: X-ray diffraction
Resolution: 1.94 Å
Organisms: Serratia sp. (strain FS14), Arabidopsis thaliana, synthetic construct
Chains: 8
Atoms: 15,412
Mol. weight: 213.86 kDa
Released: 7 Dec 2022

Explore 7VN3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VN3 contains 108 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	-362--358	5	19
α-helix	-351--337	15
β-strand	-334--330	5	19
α-helix	-325--316	10
β-strand	-309--305	5	19
α-helix	-304--302	3
α-helix	-301--296	6
β-strand	-292	1	20
α-helix	-291--289	3
α-helix	-285--282	4
β-strand	-279	1	21
α-helix	-277--272	6
β-strand	-270--269	2	22
β-strand	-266--265	2	22
β-strand	-262--257	6	19
β-strand	-254--250	5	23
β-strand	-240	1	24
α-helix	-239--237	3
α-helix	-236--227	10
β-strand	-223--221	3	23
α-helix	-214--205	10
β-strand	-201--196	6	25
β-strand	-193--186	8	25
α-helix	-182--168	15
α-helix	-158--150	9
β-strand	-146--141	6	23
α-helix	-139--137	3
α-helix	-136--131	6
β-strand	-126--123	4	23
α-helix	-122--120	3
β-strand	-119	1	24
β-strand	-118	1	26
β-strand	-115	1	26
α-helix	-111	1
β-strand	-110--109	2	27
β-strand	-108--102	7	19
β-strand	-101	1	20
α-helix	-95--90	6
α-helix	-89--84	6
α-helix	-81--72	10
β-strand	-67--66	2	19
β-strand	-64	1	21
α-helix	-63--57	7
α-helix	-53--42	12
β-strand	-40--39	2	27
α-helix	-38--37	2
α-helix	-32--17	16
α-helix	-11-21	13
α-helix	27-55	29
α-helix	65-75	11
β-strand	79-80	2	28
β-strand	86-87	2	28

Chain B: 27 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	-362--358	5	29
α-helix	-351--337	15
β-strand	-334--330	5	29
α-helix	-325--316	10
β-strand	-309--305	5	29
α-helix	-304--302	3
α-helix	-301--296	6
β-strand	-292	1	30
α-helix	-291--290	2
β-strand	-289	1	31
α-helix	-285--282	4
β-strand	-279	1	32
α-helix	-277--272	6
β-strand	-270--269	2	31
β-strand	-266--265	2	31
β-strand	-262--257	6	29
β-strand	-254--250	5	33
β-strand	-240	1	34
α-helix	-236--228	9
β-strand	-223--221	3	33
α-helix	-214--205	10
β-strand	-201--196	6	35
β-strand	-193--186	8	35
α-helix	-182--168	15
α-helix	-158--150	9
β-strand	-146--141	6	33
α-helix	-139--137	3
α-helix	-136--131	6
β-strand	-126--123	4	33
α-helix	-122--120	3
β-strand	-119	1	34
β-strand	-118	1	36
β-strand	-115	1	36
α-helix	-114--113	2
α-helix	-111	1
β-strand	-110--109	2	37
β-strand	-108--102	7	29
β-strand	-101	1	30
α-helix	-95--90	6
α-helix	-89--84	6
α-helix	-81--72	10
β-strand	-67--66	2	29
β-strand	-64	1	32
α-helix	-63--57	7
α-helix	-53--42	12
β-strand	-40--39	2	37
α-helix	-38--37	2
α-helix	-32--17	16
α-helix	-11-21	13
α-helix	22-26	5
α-helix	27-53	27
α-helix	65-75	11
β-strand	79-80	2	38
β-strand	86-87	2	38

Chain C: 28 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	-366--365	2
β-strand	-362--358	5	1
α-helix	-351--337	15
β-strand	-334--330	5	1
α-helix	-325--317	9
β-strand	-309--305	5	1
α-helix	-304--302	3
α-helix	-301--296	6
β-strand	-292	1	2
α-helix	-291--289	3
α-helix	-285--282	4
β-strand	-279	1	3
α-helix	-277--272	6
β-strand	-270--269	2	4
β-strand	-266--265	2	4
β-strand	-262--257	6	1
β-strand	-254--250	5	5
β-strand	-240	1	6
α-helix	-239--237	3
α-helix	-236--228	9
β-strand	-223--221	3	5
α-helix	-214--212	3
α-helix	-210--205	6
β-strand	-201--196	6	7
β-strand	-193--186	8	7
α-helix	-182--168	15
α-helix	-158--149	10
β-strand	-146--141	6	5
α-helix	-139--137	3
α-helix	-136--131	6
β-strand	-126--123	4	5
α-helix	-122--120	3
β-strand	-119--118	2	6
β-strand	-115--114	2	6
α-helix	-111	1
β-strand	-110--109	2	8
β-strand	-108--102	7	1
β-strand	-101	1	2
α-helix	-95--89	7
α-helix	-88--84	5
α-helix	-81--72	10
β-strand	-67--66	2	1
β-strand	-64	1	3
α-helix	-63--57	7
α-helix	-53--42	12
β-strand	-40--39	2	8
α-helix	-38--37	2
α-helix	-32--16	17
α-helix	-11-21	13
α-helix	27-54	28
α-helix	65-75	11
β-strand	79-80	2	9
β-strand	86-87	2	9

Chain D: 27 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	-361--358	4	10
α-helix	-351--337	15
β-strand	-333--330	4	10
α-helix	-325--317	9
β-strand	-309--305	5	10
α-helix	-304--302	3
α-helix	-301--296	6
β-strand	-292--291	2	10
α-helix	-290--289	2
α-helix	-285--282	4
β-strand	-279	1	11
α-helix	-277--272	6
β-strand	-270--269	2	12
β-strand	-266--265	2	12
β-strand	-262--257	6	10
β-strand	-254--250	5	13
β-strand	-240	1	14
α-helix	-239--237	3
α-helix	-236--228	9
β-strand	-223--221	3	13
α-helix	-214--205	10
β-strand	-201--196	6	15
β-strand	-193--186	8	15
α-helix	-182--168	15
α-helix	-158--150	9
β-strand	-146--141	6	13
α-helix	-139--137	3
α-helix	-136--131	6
β-strand	-126--123	4	13
α-helix	-122--120	3
β-strand	-119	1	14
β-strand	-118	1	16
β-strand	-115	1	16
α-helix	-111	1
β-strand	-110--109	2	17
β-strand	-108--101	8	10
α-helix	-95--89	7
α-helix	-88--84	5
α-helix	-81--72	10
β-strand	-67--66	2	10
β-strand	-64	1	11
α-helix	-63--57	7
α-helix	-53--42	12
β-strand	-40--39	2	17
α-helix	-38--37	2
α-helix	-32--17	16
α-helix	-11--1	11
α-helix	22-26	5
α-helix	27-54	28
α-helix	65-75	11
β-strand	79-80	2	18
β-strand	86-87	2	18

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(tptpcpapcpapcpgptpgptpgpapap*a)-3')	E, F, G, H	DNA	15	synthetic construct

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

>7VN3_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

>7VN3_2 DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3') (chains E, F, G, H)
TTCACACGTGTGAAA

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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