4F37: Colicin-E7 immunity protein

Structure of the tethered N-terminus of Alzheimer's disease A peptide. Determined by X-ray diffraction at 2.57 Å resolution. Released 15 May 2013.

Method: X-ray diffraction
Resolution: 2.57 Å
Organisms: Escherichia coli, Mus musculus
Chains: 6
Atoms: 8,769
Mol. weight: 126.38 kDa
Released: 15 May 2013

Explore 4F37 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4F37 contains 18 α-helices and 99 β-strands across 6 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	23-25	3
α-helix	28-39	12
α-helix	50-61	12
α-helix	68-71	4
α-helix	82-94	13

Chain B: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
β-strand	27	1	1
α-helix	28-40	13
α-helix	51-60	10
α-helix	66-71	6
α-helix	82-95	14
β-strand	101	1	1

Chain F: 2 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	2
β-strand	7	1	3
β-strand	11-12	2	4
β-strand	20-21	2	3
β-strand	24-25	2	2
β-strand	35-41	7	5
β-strand	48-53	6	5
β-strand	59-61	3	5
β-strand	71-74	4	3
β-strand	79-82	4	3
α-helix	89-91	3
β-strand	94-101	8	5
α-helix	107-109	3
β-strand	111-115	5	5
β-strand	120	1	5
β-strand	122-123	2	4
β-strand	129	1	6
β-strand	135	1	7
β-strand	148-149	2	8
β-strand	152-155	4	7
β-strand	158	1	6
β-strand	164	1	9
β-strand	178-182	5	7
β-strand	187-191	5	7
β-strand	194-195	2	8
β-strand	209	1	9

Chain H: 2 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	11-12	2	11
β-strand	17-24	8	10
β-strand	35-41	7	12
β-strand	48-53	6	12
β-strand	59	1	12
β-strand	69-70	2	10
β-strand	73-74	2	10
β-strand	79-85	7	10
α-helix	89-91	3
β-strand	93-100	8	12
β-strand	101	1	13
β-strand	111	1	13
β-strand	115	1	12
β-strand	119-121	3	12
β-strand	122-123	2	11
β-strand	129	1	14
β-strand	132-136	5	15
β-strand	148-155	8	15
β-strand	157	1	16
β-strand	158	1	14
β-strand	176-177	2	15
α-helix	178-180	3
β-strand	181-183	3	16
β-strand	186-188	3	16
β-strand	190-195	6	15
β-strand	207	1	17
β-strand	220	1	17

Chain K: 2 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	18
β-strand	10-12	3	19
β-strand	15	1	20
β-strand	17	1	20
β-strand	19-22	4	21
β-strand	24-25	2	18
β-strand	40-42	3	19
β-strand	53	1	19
β-strand	67-71	5	21
β-strand	76-80	5	21
β-strand	89-93	5	19
α-helix	101	1
β-strand	102	1	5
β-strand	107-110	4	19
β-strand	116	1	22
β-strand	122-123	2	23
α-helix	129-132	4
β-strand	135-141	7	23
β-strand	145	1	22
β-strand	150-152	3	24
β-strand	155	1	25
β-strand	165	1	23
β-strand	168	1	23
β-strand	180-186	7	23
β-strand	196	1	25
β-strand	200-202	3	24
β-strand	210	1	24

Chain L: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	26
β-strand	12-13	2	27
β-strand	19-25	7	26
β-strand	38-43	6	28
β-strand	51-54	4	28
β-strand	58-59	2	28
β-strand	71-72	2	26
β-strand	75-80	6	26
β-strand	89-95	7	28
β-strand	103	1	28
β-strand	107-109	3	28
β-strand	110-111	2	27
β-strand	116	1	29
β-strand	119-121	3	30
α-helix	127-129	3
β-strand	135-137	3	31
β-strand	140-144	5	30
β-strand	145	1	29
β-strand	165	1	32
β-strand	168-169	2	30
β-strand	178-181	4	30
β-strand	183	1	32
β-strand	184-186	3	31
α-helix	190-193	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Colicin-E7 immunity protein	A, B	protein	124	Escherichia coli	Q03708 (AlphaFold model)
Im7 immunity protein	F, H	protein	228	Mus musculus	P01863 (AlphaFold model)
Fab WO2 anti-amyloid-beta antibody Fab fragment	K, L	protein	219	Mus musculus	A2NHM3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4F37_1 Colicin-E7 immunity protein (chains A, B)
DAEFRHDSGYEVHHQKSELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKI
TEHPDGTDLIYYPSDNRDDSPEGIVKEIKEWRAANGKPGFKQGAAADYKDDDDKAADYKD
DDDK

Sequence of entity 2 (F, H), FASTA

>4F37_2 Im7 immunity protein (chains F, H)
QVTLKESGPGILQPSQTLSLTCSFSGFSLRTSRVGVSWIRQPSGKGLEWLAHIYWDDDKR
YNPSLESRLTISKDTSRNQVFLKITSVDTADTATYYCARRGFYGRKYEVNHFDYWGQGTT
LTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPA
VLQSDLYTLSSSVTVTSSTWPSESITCNVAHPASSTKVDKKIVPRDCG

Sequence of entity 3 (K, L), FASTA

>4F37_3 Fab WO2 anti-amyloid-beta antibody Fab fragment (chains K, L)
DIVMTQTPLSLPVSLGDQASISCRSSQTILHSNGNTYLEWYLQKPGQSPNLLIYKVSKRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSRVPLTFGAGTKLELKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Structural studies of the tethered N-terminus of the Alzheimer's disease amyloid-beta peptide. Nisbet, R.M., Nuttall, S.D., Robert, R. et al. Proteins (2013) 81:1748-1758. DOI 10.1002/prot.24312 · PubMed

Other PDB entries of the same protein (UniProt Q03708 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WNW 1.79 Å, Chaperone Spy bound to Im7 6-45 ensemble
1CEI 1.8 Å, Structure determination of the colicin E7 immunity protein (IMME7) that binds…
1UNK 1.8 Å, Structure of colicin E7 immunity protein
2JB0 1.91 Å, Crystal structure of the mutant H573A of the nuclease domain of COLE7 in complex with IM7
1AYI 2.0 Å, Colicin E7 immunity protein IM7
1MZ8 2.0 Å, Crystal structures of the nuclease domain of COLE7/IM7 in complex with a phosphate ion…
1ZNV 2.0 Å, How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal…
2ERH 2.0 Å, Crystal Structure of the E7_G/Im7_G complex; a designed interface between the colicin E7…
2JAZ 2.03 Å, Crystal structure of the mutant N560D of the nuclease domain of COLE7 in complex with IM7
1UJZ 2.1 Å, Crystal structure of the E7_C/Im7_C complex; a computationally designed interface…
2JBG 2.2 Å, crystal structure of the mutant N560A of the nuclease domain of ColE7 in complex with Im7
7CEI 2.3 Å, The endonuclease domain of colicin E7 in complex with its inhibitor IM7 protein

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