1D3E: Human rhinovirus 16

cryo-EM structure of human rhinovirus 16 (HRV16) complexed with a two-domain fragment of its cellular receptor, intercellular adhesion molecule-1 (D1D2-icam-1). Implications for virus-receptor interactions. Alpha carbons only. Determined by electron microscopy at 28.0 Å resolution. Released 19 Jan 2000.

Method: Electron microscopy
Resolution: 28.0 Å
Organisms: Homo sapiens, Human rhinovirus sp.
Chains: 5
Atoms: 989
Mol. weight: 114.35 kDa
Released: 19 Jan 2000

Explore 1D3E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1D3E contains 12 α-helices and 44 β-strands across 5 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 1: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	66-72	7
β-strand	75-83	9	11
β-strand	93-97	5	12
α-helix	98-101	4
α-helix	104-110	7
β-strand	112-130	19	11
β-strand	137-145	9	12
α-helix	158-162	5
β-strand	165-171	7	12
β-strand	177-192	16	11
β-strand	216-221	6	12
β-strand	230-248	19	11

Chain 2: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	21
β-strand	21-25	5	21
α-helix	56-59	4
β-strand	69-71	3	22
β-strand	78-82	5	23
α-helix	90-98	9
β-strand	99-111	13	22
β-strand	119-128	10	23
α-helix	179-184	6
β-strand	187-191	5	23
β-strand	196-202	7	22
β-strand	219-230	12	23
β-strand	238-254	17	22

Chain 3: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	31
α-helix	44-47	4
β-strand	69-72	4	32
β-strand	78-87	10	33
α-helix	98-103	6
β-strand	106-119	14	32
β-strand	128-134	7	33
α-helix	143-148	6
β-strand	151-156	6	33
β-strand	162-167	6	32
β-strand	188-193	6	33
β-strand	207-224	18	32

Chain 4: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	41
β-strand	23-30	8	41

Chain I: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
β-strand	8-12	5	2
β-strand	17-23	7	1
β-strand	30-34	5	3
β-strand	38-42	5	1
β-strand	49-55	7	1
β-strand	64-68	5	3
β-strand	73-77	5	3
β-strand	79-83	5	2
β-strand	88-91	4	4
α-helix	116-118	3
β-strand	119-125	7	5
β-strand	128-134	7	5
β-strand	140-147	8	4
β-strand	157-164	8	5
α-helix	166-168	3
β-strand	172-176	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (intercellular adhesion molecule-1)	I	protein	185	Homo sapiens	P05362 (AlphaFold model)
Protein (rhinovirus 16 coat protein VP1)	1	protein	285	Human rhinovirus sp.	Q82122 (AlphaFold model)
Protein (rhinovirus 16 coat protein VP2)	2	protein	252	Human rhinovirus sp.	Q82122 (AlphaFold model)
Protein (rhinovirus 16 coat protein VP3)	3	protein	238	Human rhinovirus sp.	Q82122 (AlphaFold model)
Protein (rhinovirus 16 coat protein VP4)	4	protein	68	Human rhinovirus sp.	Q82122 (AlphaFold model)

Sequence of entity 1 (I), FASTA

>1D3E_1 PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) (chains I)
QTSVSPSKVILPRGGSVLVTCSTSCDQPKLLGIETPLPKKELLLPGNNRKVYELSNVQED
SQPMCYSNCPDGQSTAKTFLTVYWTPERVELAPLPSWQPVGKNLTLRCQVEGGAPRANLT
VVLLRGEKELKREPAVGEPAEVTTTVLVRRDHHGANFSCRTELDLRPQGLELFENTSAPY
QLQTF

Sequence of entity 2 (1), FASTA

>1D3E_2 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1) (chains 1)
APVAAYVDEVLNEVLVVPNINQSHPTTSNAAPVLDAAETGHTNKIQPEDTIETRYVQSSQ
TLDEMSVESFLGRSGCIHESVLDIVDNYNDQSFTKWNINLQEMAQIRRKFEMFTYARFDS
EITMVPSVAAKDGHIGHIVMQYMYVPPGAPIPTTRDDYAWQSGTNASVFWQHGQPFPRFS
LPFLSIASAYYMFYDGYDGDTYKSRYGTVVTNDMGTLCSRIVTSEQLHKVKVVTRIYHKA
KHTKAWCPRPPRAVQYSHTHTTNYKLSSEVHNDVAIRPRTNLTTV

Sequence of entity 3 (2), FASTA

>1D3E_3 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2) (chains 2)
SDRIIQITRGDSTITSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSSNRFYTLDSK
MWNSTSKGWWWKLPDALKDMGIFGENMFYHFLGRSGYTVHVQCNASKFHQGTLLVVMIPE
HQLATVNKGNVNAGYKYTHPGEAGREVGTAAAAEKQPSDDNWLNFDGTLLGNLLIFPHQF
INLRSNNSATLIVPYVNAVPMDSMVRHNNWSLVIIPVCQLQSNNISNIVPITVSISPMCA
EFSGARAKTVVQ

Sequence of entity 4 (3), FASTA

>1D3E_4 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3) (chains 3)
GLPVYVTPGSGQFMTTDDMQSPCALPWYHPTKEIFIPGEVKNLIEMCQVDTLIPINSTQS
NIGNVSMYTVTLSPQTKLAEEIFAIKVDIASHPLATTLIGEIASYFTHWTGSLRFSFMFC
GTANTTLKVLLAYTPPGIGKPRSRKEAMLGTHVVWDVGLQSTVSLVVPWISASQYRFTTP
DTYSSAGYITCWYQTNFVVPPNTPNTAEMLCFVSGCKDFCLRMARDTDLHKQTGPITQ

Sequence of entity 5 (4), FASTA

>1D3E_5 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4) (chains 4)
GAQVSRQNVGTHSTQNMVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVL
EKGIPTLQ

Primary citation

Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor. Kolatkar, P.R., Bella, J., Olson, N.H. et al. EMBO J (1999) 18:6249-6259. DOI 10.1093/emboj/18.22.6249 · PubMed

Other PDB entries of the same protein (UniProt P05362 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1IAM 2.1 Å, Structure of the two amino-terminal domains of human intercellular adhesion molecule-1,…
7BG7 2.4 Å, HRV14 in complex with its receptor ICAM-1
2OZ4 2.7 Å, Structural Plasticity in IgSF Domain 4 of ICAM-1 Mediates Cell Surface Dimerization
5MZA 2.78 Å, The DBLb domain of PF11_0521 PfEMP1 bound to human ICAM-1
1IC1 3.0 Å, The crystal structure for the N-terminal two domains of icam-1
1P53 3.06 Å, The Crystal Structure of ICAM-1 D3-D5 fragment
1D3L 3.25 Å, D1D2-icam-1 fully glycosylated, variation of D1-D2 interdomain angle in different…
1MQ8 3.3 Å, Crystal structure of alphaL I domain in complex with ICAM-1
3TCX 3.6 Å, Structure of Engineered Single Domain ICAM-1 D1 with High-Affinity aL Integrin I Domain…
6S8U 3.67 Å, Structure of the PfEMP1 IT4var13 DBLbeta domain bound to ICAM-1
6EIT 3.9 Å, Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1
1Z7Z 8.0 Å, Cryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi

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