1K5M: Coat protein VP1

Name: PDB 1K5M: Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus MN-III-2
Published: 2002-07-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus MN-III-2. Determined by X-ray diffraction at 2.7 Å resolution. Released 17 Jul 2002.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Human rhinovirus 14, Human immunodeficiency virus type 1 group M subtype B (isolate MN)
Chains: 4
Atoms: 7,117
Mol. weight: 96.38 kDa
Ligands: SPH
Released: 17 Jul 2002

Explore 1K5M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1K5M contains 41 α-helices and 61 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: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	1013-1015	3
α-helix	1016-1017	2
β-strand	1018-1020	3	1
β-strand	1023	1	2
β-strand	1034-1035	2	3
α-helix	1037-1039	3
α-helix	1047-1049	3
β-strand	1053	1	2
β-strand	1056-1057	2	1
α-helix	1063-1065	3
β-strand	1066	1	4
α-helix	1067-1070	4
β-strand	1075-1084	10	5
β-strand	1099-1103	5	6
α-helix	1110-1116	7
β-strand	1119-1135	17	5
β-strand	1147-1153	7	6
α-helix	1158-1160	3
α-helix	1166-1169	4
β-strand	1175-1179	5	6
β-strand	1180	1	7
β-strand	1182	1	7
β-strand	1183-1188	6	5
β-strand	1197-1198	2	5
β-strand	1203	1	8
β-strand	1204-1206	3	9
β-strand	1211-1213	3	9
α-helix	1215-1217	3
β-strand	1223-1228	6	6
β-strand	1237-1255	19	5
α-helix	1257-1258	2
β-strand	1259	1	10
α-helix	1262-1263	2
α-helix	1275-1277	3
α-helix	1280-1282	3

Chain B: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	1314-1318	5	11
β-strand	1321-1325	5	11
β-strand	1332-1333	2	12
α-helix	1334-1336	3
α-helix	1341-1343	3
α-helix	1344-1346	3
α-helix	1352-1353	2
β-strand	1354	1	12
α-helix	1357-1359	3
β-strand	1364-1365	2	12
β-strand	1369-1372	4	13
β-strand	1378-1382	5	14
α-helix	1384-1386	3
α-helix	1390-1398	9
β-strand	1399-1411	13	12
β-strand	1419-1428	10	14
α-helix	1432-1433	2
β-strand	1434	1	15
α-helix	1444-1447	4
α-helix	1450-1452	3
β-strand	1454-1455	2	14
α-helix	1456-1458	3
α-helix	1479	1
β-strand	1480	1	15
α-helix	1481	1
α-helix	1484-1486	3
β-strand	1491	1	10
α-helix	1493-1498	6
β-strand	1501-1505	5	14
β-strand	1511-1516	6	12
β-strand	1525	1	12
β-strand	1530	1	8
β-strand	1533-1544	12	14
α-helix	1545-1546	2
β-strand	1552-1555	4	13
β-strand	1556-1569	14	12
α-helix	1572-1573	2

Chain C: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	1606-1607	2
β-strand	1623	1	5
α-helix	1630-1633	4
β-strand	1639-1640	2	5
β-strand	1642	1	4
α-helix	1643-1646	4
β-strand	1651-1652	2	3
α-helix	1664-1667	4
β-strand	1669-1671	3	3
β-strand	1673	1	16
β-strand	1679-1684	6	17
α-helix	1690-1692	3
α-helix	1696-1701	6
β-strand	1704-1708	5	18
β-strand	1711-1717	7	3
β-strand	1724	1	19
β-strand	1726-1732	7	17
α-helix	1742-1746	5
β-strand	1749-1754	6	17
β-strand	1760-1765	6	3
β-strand	1774-1775	2	18
β-strand	1786-1791	6	17
β-strand	1795	1	16
β-strand	1796	1	19
α-helix	1797-1798	2
β-strand	1805-1813	9	3
β-strand	1818-1822	5	18

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	1935-1937	3
α-helix	1950-1953	4
β-strand	1956	1	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coat protein VP1 (P1D)	A	protein	289	Human rhinovirus 14	P03303 (AlphaFold model)
CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120	B	protein	277	Human rhinovirus 14, Human immunodeficiency virus type 1 group M subtype B (isolate MN)	P03303 (AlphaFold model), P05877
Coat protein VP3 (P1C)	C	protein	236	Human rhinovirus 14	P03303 (AlphaFold model)
Coat protein VP4 (P1A)	D	protein	68	Human rhinovirus 14	P03303 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1K5M_1 COAT PROTEIN VP1 (P1D) (chains A)
GLGDELEEVIVEKTKQTVASISSGPKHTQKVPILTANETGATMPVLPSDSIETRTTYMHF
NGSETDVECFLGRAACVHVTEIQNKDATGIDNHREAKLFNDWKINLSSLVQLRKKLELFT
YVRFDSEYTILATASQPDSANYSSNLVVQAMYVPPGAPNPKEWDDYTWQSASNPSVFFKV
GDTSRFSVPYVGLASAYNCFYDGYSHDDAETQYGITVLNHMGSMAFRIVNEHDEHKTLVK
IRVYHRAKHVEAWIPRAPRALPYTSIGRTNYPKNTEPVIKKRKGDIKSY

Sequence of entity 2 (B), FASTA

>1K5M_2 CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120 (chains B)
SPNVEACGYSDRVQQITLGNSTITTQEAANAVVCYAEWPEYLPDVDASDVNKTSKPDTSV
CRFYTLDSKTWTTGSKGWCWKLPDALKDMGVFGQNMFFHSLGRSGYTVHVQCNATKFHSG
CLLVVVIPEHQLASHEGGNVSVKYTFTHPGERGIDLSSAADTIGPGRAFYTTKNNEVGGP
VKDVIYNMNGTLLGNLLIFPHQFINLRTNNTATIVIPYINSVPIDSMTRHNNVSLMVIPI
APLTVPTGATPSLPITVTIAPMCTEFSGIRSKSIVPQ

Sequence of entity 3 (C), FASTA

>1K5M_3 COAT PROTEIN VP3 (P1C) (chains C)
GLPTTTLPGSGQFLTTDDRQSPSALPNYEPTPRIHIPGKVHNLLEIIQVDTLIPMNNTHT
KDEVNSYLIPLNANRQNEQVFGTNLFIGDGVFKTTLLGEIVQYYTHWSGSLRFSLMYTGP
ALSSAKLILAYTPPGARGPQDRREAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYTDPDT
YTSAGFLSCWYQTSLILPPETTGQVYLLSFISACPDFKLRLMKDTQTISQTVALTE

Sequence of entity 4 (D), FASTA

>1K5M_4 COAT PROTEIN VP4 (P1A) (chains D)
GAQVSTQKSGSHENQNILTNGSNQTFTVINYYKDAASTSSAGQSLSMDPSKFTEPVKDLM
LKGAPALN

Ligands and cofactors

ID	Name	Formula	Copies
SPH	Sphingosine	C18 H37 N O2	1

Primary citation

Crystal Structure of a Human Rhinovirus that Displays Part of the HIV-1 V3 Loop and Induces Neutralizing Antibodies against HIV-1. Ding, J., Smith, A.D., Geisler, S.C. et al. Structure (2002) 10:999-1011. DOI 10.1016/S0969-2126(02)00793-1 · PubMed

Other PDB entries of the same protein (UniProt P03303 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KYZ 1.84 Å, HRV14 3C in complex with single chain antibody YDF
9LGP 2.11 Å, Crystal structure of the HRV B14 3C protease in complex with AG7404
5W3M 2.26 Å, CryoEM structure of rhinovirus B14 in complex with C5 Fab (33 degrees Celsius, molar…
6KZ0 2.4 Å, HRV14 3C in complex with single chain antibody GGVV
7BG7 2.4 Å, HRV14 in complex with its receptor ICAM-1
1NCQ 2.5 Å, The structure of HRV14 when complexed with pleconaril, an antiviral compound
5W3E 2.53 Å, CryoEM structure of rhinovirus B14 in complex with C5 Fab (33 degrees Celsius, molar…
7BG6 2.6 Å, HRV14 native particle solved by cryoEM
31LE 2.64 Å, HRV E1007A mutant
31LF 2.71 Å, HRV virion E2250A mutant
5W3L 2.71 Å, CryoEM structure of rhinovirus B14 in complex with C5 Fab (4 degrees Celsius, molar…
29UB 2.73 Å, HRV B14 virion

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