8H64: Internalin A

Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH24 bound. Determined by X-ray diffraction at 2.35 Å resolution. Released 4 Oct 2023.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Listeria monocytogenes serovar 1/2a, Lama glama
Chains: 8
Atoms: 18,415
Mol. weight: 253.72 kDa
Released: 4 Oct 2023

Explore 8H64 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H64 contains 100 α-helices and 168 β-strands across 8 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.

Chains A and G: 22 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	42-43	2	1
α-helix	44-47	4
α-helix	51-60	10
β-strand	69-70	2	1
α-helix	72-75	4
β-strand	80-82	3	2
α-helix	94-96	3
β-strand	102-104	3	2
α-helix	114-116	3
β-strand	124-126	3	2
α-helix	136-138	3
β-strand	146-148	3	2
α-helix	158-160	3
β-strand	168-176	9	2
α-helix	180-182	3
β-strand	190-195	6	2
α-helix	201-203	3
β-strand	211-213	3	2
α-helix	223-227	5
β-strand	233-235	3	2
α-helix	245-249	5
β-strand	255-257	3	2
α-helix	267-271	5
β-strand	277-279	3	2
α-helix	289-291	3
β-strand	299-301	3	2
α-helix	311-313	3
β-strand	321-323	3	2
α-helix	333-337	5
β-strand	343-345	3	2
α-helix	355-359	5
β-strand	365-367	3	2
α-helix	377-379	3
β-strand	387-389	3	2
β-strand	397	1	3
α-helix	399-401	3
β-strand	409-411	3	2
β-strand	415-418	4	4
α-helix	419-421	3
β-strand	422-423	2	5
β-strand	427-431	5	6
β-strand	435	1	3
α-helix	440	1
β-strand	441	1	3
α-helix	442-444	3
β-strand	446-447	2	4
α-helix	448-450	3
β-strand	452-454	3	6
β-strand	457-461	5	6
β-strand	468-479	12	4
β-strand	482-493	12	4
β-strand	494-495	2	5

Chains B, D, F and H: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	32-39	8	9
β-strand	46-52	7	9
β-strand	55-58	4	9
α-helix	60-62	3
β-strand	66-71	6	7
β-strand	76-81	6	7
α-helix	86-88	3
β-strand	90-98	9	9
β-strand	111	1	9
β-strand	117-119	3	9
β-strand	120-121	2	8

Chain C: 22 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	42-43	2	10
α-helix	44-47	4
α-helix	51-60	10
β-strand	69-70	2	10
α-helix	72-75	4
β-strand	80-82	3	11
α-helix	94-96	3
β-strand	102-104	3	11
α-helix	114-116	3
β-strand	124-126	3	11
α-helix	136-138	3
β-strand	146-148	3	11
α-helix	158-160	3
β-strand	168-176	9	11
α-helix	180-182	3
β-strand	190-195	6	11
α-helix	201-203	3
β-strand	211-213	3	11
α-helix	223-227	5
β-strand	233-235	3	11
α-helix	245-249	5
β-strand	255-257	3	11
α-helix	267-271	5
β-strand	277-279	3	11
α-helix	289-291	3
β-strand	299-301	3	11
α-helix	311-313	3
β-strand	321-323	3	11
α-helix	333-337	5
β-strand	343-345	3	11
α-helix	355-359	5
β-strand	365-367	3	11
α-helix	377-381	5
β-strand	387-389	3	11
β-strand	397	1	12
α-helix	399-401	3
β-strand	409-411	3	11
β-strand	415-418	4	13
α-helix	419-421	3
β-strand	422-423	2	14
β-strand	429-431	3	15
β-strand	435	1	12
α-helix	440	1
β-strand	441	1	12
α-helix	442-444	3
β-strand	446-447	2	13
α-helix	448-450	3
β-strand	452-454	3	15
β-strand	457-459	3	15
β-strand	468-479	12	13
β-strand	482-493	12	13
β-strand	494-495	2	14

Chain E: 22 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	42-43	2	19
α-helix	44-47	4
α-helix	51-60	10
β-strand	69-70	2	19
α-helix	72-75	4
β-strand	80-82	3	20
α-helix	94-96	3
β-strand	102-104	3	20
α-helix	114-116	3
β-strand	124-126	3	20
α-helix	136-138	3
β-strand	146-148	3	20
α-helix	158-160	3
β-strand	168-176	9	20
α-helix	180-182	3
β-strand	190-195	6	20
α-helix	201-203	3
β-strand	211-213	3	20
α-helix	223-227	5
β-strand	233-235	3	20
α-helix	245-249	5
β-strand	255-257	3	20
α-helix	267-271	5
β-strand	277-279	3	20
α-helix	289-291	3
β-strand	299-301	3	20
α-helix	311-313	3
β-strand	321-323	3	20
α-helix	333-337	5
β-strand	343-345	3	20
α-helix	355-359	5
β-strand	365-367	3	20
α-helix	377-379	3
β-strand	387-389	3	20
β-strand	397	1	21
α-helix	399-401	3
β-strand	409-411	3	20
β-strand	415-418	4	22
α-helix	419-421	3
β-strand	422-423	2	23
β-strand	429-431	3	24
β-strand	435	1	21
α-helix	440	1
β-strand	441	1	21
α-helix	442-444	3
β-strand	446-447	2	22
α-helix	448-450	3
β-strand	452-454	3	24
β-strand	457-459	3	24
β-strand	468-479	12	22
β-strand	482-493	12	22
β-strand	494-495	2	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Internalin A	A, C, E, G	protein	462	Listeria monocytogenes serovar 1/2a	P0DJM0 (AlphaFold model)
Anti-internalin A VHH24	B, D, F, H	protein	123	Lama glama

Sequence of entity 1 (A, C, E, G), FASTA

>8H64_1 Internalin A (chains A, C, E, G)
SATITQDTPINQIFTDTALAEKMKTVLGKTNVTDTVSQTDLDQVTTLQADRLGIKSIDGV
EYLNNLTQINFSNNQLTDITPLKNLTKLVDILMNNNQIADITPLANLTNLTGLTLFNNQI
TDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLKPLANLTTLERLDI
SSNKVSDISVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIGTLASLTN
LTDLDLANNQISNLAPLSGLTKLTELKLGANQISNISPLAGLTALTNLELNENQLEDISP
ISNLKNLTYLTLYFNNISDISPVSSLTKLQRLFFYNNKVSDVSSLANLTNINWLSAGHNQ
ISDLTPLANLTRITQLGLNDQAWTNAPVNYKANVSIPNTVKNVTGALIAPATISDGGSYT
EPDITWNLPSYTNEVSYTFSQPVTIGKGTTTFSGTVTQPLKA

Sequence of entity 2 (B, D, F, H), FASTA

>8H64_2 Anti-internalin A VHH24 (chains B, D, F, H)
EVQLVESGGGLVQPGGSLRLSCAASGFTLDRYAIGWFRQAPGKEREGVSVISDTITAYRN
SVKGRFTISRDNAKNTVYLQMNRLKPEDTAIYYCAVRDRGRVYSSTWSGFGSWGQGTQVT
ISS

Primary citation

Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes. Yamazaki, T., Nagatoishi, S., Yamawaki, T. et al. J Biol Chem (2023) 299:105254-105254. DOI 10.1016/j.jbc.2023.105254 · PubMed

Other PDB entries of the same protein (UniProt P0DJM0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1O6V 1.5 Å, Internalin (INLA, Listeria monocytogenes) - functional domain, uncomplexed
8H63 1.53 Å, Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH10 bound
1O6T 1.6 Å, Internalin (INLA, Listeria monocytogenes) - functional domain, uncomplexed
2OMZ 1.6 Å, Crystal structure of InlA Y369A/hEC1 complex
2OMY 1.7 Å, Crystal structure of InlA S192N/hEC1 complex
1O6S 1.8 Å, Internalin (Listeria monocytogenes) / E-Cadherin (human) Recognition Complex
2OMU 1.8 Å, Crystal structure of InlA G194S+S Y369S/hEC1 complex
2OMW 1.85 Å, Crystal structure of InlA S192N Y369S/mEC1 complex
2OMV 1.9 Å, Crystal structure of InlA S192N Y369S/hEC1 complex
8H62 1.91 Å, Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12

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