4IRL: CARD domain of zebrafish GBP-NLRP1 like protein

X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein. Determined by X-ray diffraction at 1.47 Å resolution. Released 7 Aug 2013.

Method: X-ray diffraction
Resolution: 1.47 Å
Organisms: Escherichia coli, Danio rerio
Chains: 3
Atoms: 12,984
Mol. weight: 159.95 kDa
Ligands: MLI
Released: 7 Aug 2013

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

Secondary structure: helices and β-sheets

4IRL contains 88 α-helices and 73 β-strands across 3 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: 30 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	1
α-helix	18-32	15
β-strand	35-39	5	1
α-helix	44-52	9
β-strand	60-64	5	1
α-helix	65-67	3
α-helix	68-73	6
β-strand	77	1	2
α-helix	78-79	2
β-strand	80	1	3
α-helix	84-87	4
β-strand	90	1	4
α-helix	92-97	6
β-strand	99-100	2	3
β-strand	103-104	2	3
β-strand	107-112	6	1
β-strand	115-119	5	5
β-strand	129	1	6
α-helix	130-132	3
α-helix	133-142	10
β-strand	146-148	3	5
α-helix	155-164	10
β-strand	168-173	6	7
β-strand	176-183	8	7
α-helix	187-201	15
α-helix	211-219	9
β-strand	223-228	6	5
α-helix	230-232	3
α-helix	233-239	7
β-strand	243-246	4	5
α-helix	247-249	3
β-strand	250	1	6
β-strand	251	1	8
β-strand	254	1	8
α-helix	255-256	2
α-helix	258	1
β-strand	259-260	2	9
β-strand	261-267	7	1
β-strand	268	1	2
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	1
β-strand	305	1	4
α-helix	306-312	7
α-helix	316-327	12
β-strand	329-330	2	9
α-helix	331-332	2
α-helix	337-353	17
α-helix	358-381	24
α-helix	383-389	7
α-helix	393-402	10
α-helix	408-416	9
α-helix	420-449	30
α-helix	451-461	11

Chain B: 29 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	10
α-helix	18-32	15
β-strand	35-39	5	10
α-helix	44-52	9
β-strand	60-64	5	10
α-helix	65-67	3
α-helix	68-73	6
β-strand	77	1	11
α-helix	78-79	2
β-strand	80	1	12
α-helix	84-87	4
β-strand	90	1	13
α-helix	92-97	6
β-strand	99-100	2	12
β-strand	103-104	2	12
β-strand	107-112	6	10
β-strand	115-119	5	14
β-strand	129	1	15
α-helix	130-132	3
α-helix	133-141	9
β-strand	146-148	3	14
α-helix	155-164	10
β-strand	168-173	6	16
β-strand	176-183	8	16
α-helix	187-201	15
α-helix	211-219	9
β-strand	223-228	6	14
α-helix	230-232	3
α-helix	233-239	7
β-strand	243-246	4	14
α-helix	247-249	3
β-strand	250-251	2	15
β-strand	254-255	2	15
α-helix	258	1
β-strand	259-260	2	17
β-strand	261-267	7	10
β-strand	268	1	11
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	10
β-strand	305	1	13
α-helix	306-312	7
α-helix	316-327	12
β-strand	329-330	2	17
α-helix	331-332	2
α-helix	337-353	17
α-helix	358-381	24
α-helix	383-389	7
α-helix	393-402	10
α-helix	408-416	9
α-helix	420-449	30
α-helix	451-462	12

Chain C: 29 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	4	1
β-strand	8-11	4	18
α-helix	18-32	15
β-strand	36-39	4	18
α-helix	44-52	9
β-strand	60-64	5	18
α-helix	65-67	3
α-helix	68-73	6
β-strand	77	1	19
α-helix	78-79	2
β-strand	80	1	20
α-helix	84-87	4
β-strand	90	1	21
α-helix	92-97	6
β-strand	99-100	2	20
β-strand	103-104	2	20
β-strand	107-112	6	18
β-strand	115-119	5	22
β-strand	129	1	23
α-helix	130-132	3
α-helix	133-141	9
β-strand	146-148	3	22
α-helix	155-164	10
β-strand	168-173	6	24
β-strand	176-183	8	24
α-helix	187-201	15
α-helix	211-219	9
β-strand	223-228	6	22
α-helix	230-232	3
α-helix	233-239	7
β-strand	243-246	4	22
α-helix	247-249	3
β-strand	250-251	2	23
β-strand	254-255	2	23
β-strand	259-260	2	25
β-strand	261-267	7	18
β-strand	268	1	19
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	18
β-strand	305	1	21
α-helix	306-312	7
α-helix	316-327	12
β-strand	329-330	2	25
α-helix	331-332	2
α-helix	337-353	17
α-helix	358-381	24
α-helix	383-389	7
α-helix	393-402	10
α-helix	408-416	9
α-helix	420-449	30
α-helix	451-460	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose-binding periplasmic protein, Novel protein similar to vertebrate guanylate binding protein…	A, B, C	protein	476	Escherichia coli, Danio rerio	B0V1H4 (AlphaFold model), P0AEX9 (AlphaFold model)

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

>4IRL_1 Maltose-binding periplasmic protein, Novel protein similar to vertebrate guanylate binding protein family (chains A, B, C)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSA
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDA
ALAAAQTNAARAAAASEFVDALRGDLIQKVSSVMAIADSLMSERMITDELYSEVHYADTN
QRKMRLLFRALDSGGASVKAEFYRLLMENEPRLVHELESRHSESSGPQLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	3

Water and common crystallization additives (ACT, PEG, NA, EDO) are not listed.

Primary citation

Structure of the caspase-recruitment domain from a zebrafish guanylate-binding protein. Jin, T., Huang, M., Smith, P. et al. Acta Crystallogr Sect F Struct Biol Cryst Commun (2013) 69:855-860. DOI 10.1107/S1744309113015558 · PubMed

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