4LQW: HIV-1 capsid N-terminal domain

Crystal structure of HIV-1 capsid N-terminal domain in complex with NUP358 cyclophilin. Determined by X-ray diffraction at 1.95 Å resolution. Released 14 Aug 2013.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Homo sapiens, Human immunodeficiency virus type 1
Chains: 4
Atoms: 5,271
Mol. weight: 71.84 kDa
Released: 14 Aug 2013

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

Secondary structure: helices and β-sheets

4LQW contains 27 α-helices and 30 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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	1
β-strand	15-24	10	1
α-helix	30-41	12
β-strand	52	1	1
β-strand	55-57	3	1
β-strand	61-64	4	1
β-strand	77	1	2
β-strand	80	1	2
β-strand	83	1	3
β-strand	97-100	4	1
β-strand	108	1	3
β-strand	112-115	4	1
α-helix	120-122	3
β-strand	128-134	7	1
α-helix	136-143	8
β-strand	156-163	8	1

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	4
β-strand	15-24	10	4
α-helix	30-41	12
β-strand	52	1	4
β-strand	55-57	3	4
β-strand	61-64	4	4
β-strand	77	1	5
β-strand	80	1	5
β-strand	83	1	6
β-strand	97-100	4	4
β-strand	108	1	6
β-strand	112-115	4	4
α-helix	120-122	3
β-strand	128-134	7	4
α-helix	136-144	9
β-strand	156-163	8	4

Chain C: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	7
β-strand	10-12	3	7
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-42	7
α-helix	49-58	10
α-helix	63-83	21
α-helix	85-88	4
α-helix	90-92	3
α-helix	97-100	4
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-145	20

Chain D: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	8
β-strand	11-12	2	8
α-helix	14-16	3
α-helix	17-29	13
α-helix	36-42	7
α-helix	49-58	10
α-helix	63-83	21
α-helix	90-92	3
α-helix	97-100	4
α-helix	101-104	4
α-helix	111-119	9
α-helix	126-143	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 SUMO-protein ligase RanBP2	A, B	protein	177	Homo sapiens	P49792
Capsid protein p24	C, D	protein	146	Human immunodeficiency virus type 1	P12497

Sequence of entity 1 (A, B), FASTA

>4LQW_1 E3 SUMO-protein ligase RanBP2 (chains A, B)
MAHHHHHHMELSKETNPVVFFDVCADGEPLGRITMELFSNIVPRTAENFRALCTGEKGFG
FKNSIFHRVIPDFVCQGGDITKHDGTGGQSIYGDKFEDENFDVKHTGPGLLSMANQGQNT
NNSQFVITLKKAEHLDFKHVVFGFVKDGMDTVKKIESFGSPKGSVCRRITITECGQI

Sequence of entity 2 (C, D), FASTA

>4LQW_2 Capsid protein p24 (chains C, D)
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVG
GHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH
NPPIPVGEIYKRWIILGLNKIVRMYS

Primary citation

HIV-1 capsid undergoes coupled binding and isomerization by the nuclear pore protein NUP358. Bichel, K., Price, A.J., Schaller, T. et al. Retrovirology (2013) 10:81-81. DOI 10.1186/1742-4690-10-81 · PubMed

Other PDB entries of the same protein (UniProt P49792), best resolution first:

7MNK 1.1 Å, Crystal structure of the tetramerization element of NUP358/RanBP2 (residues 805-832)
4GA0 1.15 Å, Structure of the N-terminal domain of Nup358
4I9Y 1.75 Å, Structure of the C-terminal domain of Nup358
7MNR 1.8 Å, Crystal Structure of the ZnF3 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP
7MNV 1.8 Å, Crystal Structure of the ZnF8 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP
7MNU 2.0 Å, Crystal Structure of the ZnF7 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP
7MNP 2.05 Å, Crystal Structure of the ZnF2 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP
7MNQ 2.05 Å, Crystal Structure of the ZnF2 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP
7MNS 2.1 Å, Crystal Structure of the ZnF4 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP
3UIP 2.29 Å, Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from RanBP2 containing IR2…
7MNZ 2.35 Å, Crystal Structure of Nup358/RanBP2 Ran-binding domain 4 in complex with Ran-GPPNHP
7MNW 2.4 Å, Crystal Structure of Nup358/RanBP2 Ran-binding domain 1 in complex with Ran-GPPNHP

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