1D3I: Human rhinovirus 14

cryo-EM structure of human rhinovirus 14 (HRV14) 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 26.0 Å resolution. Released 19 Jan 2000.

Method: Electron microscopy
Resolution: 26.0 Å
Organisms: Homo sapiens, Human rhinovirus sp.
Chains: 5
Atoms: 989
Mol. weight: 114.92 kDa
Released: 19 Jan 2000

Explore 1D3I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1D3I contains 11 α-helices and 54 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 1: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	66-72	7
β-strand	75-84	10	21
β-strand	75-84	10	11
β-strand	100-104	5	11
α-helix	110-119	10
β-strand	120-135	16	11
β-strand	120-135	16	21
β-strand	146-153	8	11
α-helix	165-170	6
β-strand	174-180	7	11
β-strand	182-188	7	11
β-strand	197-200	4	21
β-strand	222-229	8	11
β-strand	237-254	18	11
β-strand	237-254	18	21

Chain 2: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	12-18	7	12
β-strand	21-28	8	12
α-helix	56-61	6
β-strand	64-71	8	12
β-strand	64-71	8	22
β-strand	77-82	6	12
α-helix	89-99	11
β-strand	100-112	13	12
β-strand	100-112	13	22
β-strand	119-127	9	12
α-helix	177-184	8
β-strand	185-191	7	12
β-strand	195-201	7	12
β-strand	210-212	3	22
β-strand	218-229	12	12
β-strand	238-253	16	12
β-strand	238-253	16	22

Chain 3: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	42-49	8
β-strand	51-53	3	13
β-strand	69-71	3	23
β-strand	81-85	5	13
α-helix	95-104	10
β-strand	105-118	14	13
β-strand	105-118	14	23
β-strand	124-132	9	13
α-helix	141-148	8
β-strand	149-155	7	13
β-strand	159-165	7	13
β-strand	174-176	3	23
β-strand	185-196	12	13
β-strand	205-221	17	23
β-strand	205-221	17	13

Chain I: 2 helices, 16 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
β-strand	103-111	9	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 14 coat protein VP1)	1	protein	289	Human rhinovirus sp.	P03303 (AlphaFold model)
Protein (rhinovirus 14 coat protein VP2)	2	protein	262	Human rhinovirus sp.	P03303 (AlphaFold model)
Protein (rhinovirus 14 coat protein VP3)	3	protein	236	Human rhinovirus sp.	P03303 (AlphaFold model)
Protein (rhinovirus 14 coat protein VP4)	4	protein	68	Human rhinovirus sp.	P03303 (AlphaFold model)

Sequence of entity 1 (I), FASTA

>1D3I_1 PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) (chains I)
QTSVSPSKVILPRGGSVLVTCSTSCDQPKLLGIETPLPKKELLLPGNNRKVYELSNVQED
SQPMCYSNCPDGQSTAKTFLTVYWTPERVELAPLPSWQPVGKNLTLRCQVEGGAPRANLT
VVLLRGEKELKREPAVGEPAEVTTTVLVRRDHHGANFSCRTELDLRPQGLELFENTSAPY
QLQTF

Sequence of entity 2 (1), FASTA

>1D3I_2 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1) (chains 1)
GLGDELEEVIVEKTKQTVASISSGPKHTQKVPILTANETGATMPVLPSDSIETRTTYMHF
NGSETDVECFLGRAACVHVTEIQNKDATGIDNHREAKLFNDWKINLSSLVQLRKKLELFT
YVRFDSEYTILATASQPDSANYSSNLVVQAMYVPPGAPNPKEWDDYTWQSASNPSVFFKV
GDTSRFSVPYVGLASAYNCFYDGYSHDDAETQYGITVLNHMGSMAFRIVNEHDEHKTLVK
IRVYHRAKHVEAWIPRAPRALPYTSIGRTNYPKNTEPVIKKRKGDIKSY

Sequence of entity 3 (2), FASTA

>1D3I_3 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2) (chains 2)
SPNVEACGYSDRVQQITLGNSTITTQEAANAVVCYAEWPEYLPDVDASDVNKTSKPDTSV
CRFYTLDSKTWTTGSKGWCWKLPDALKDMGVFGQNMFFHSLGRSGYTVHVQCNATKFHSG
CLLVVVIPEHQLASHEGGNVSVKYTFTHPGERGIDLSSANEVGGPVKDVLYNMNGTLLGN
LLIFPHQFINLRTNNTATIVIPYINSVPIDSMTRHNNVSLMVIPIAPLTVPTGATPSLPI
TVTIAPMCTEFSGIRSKSIVPQ

Sequence of entity 4 (3), FASTA

>1D3I_4 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3) (chains 3)
GLPTTTLPGSGQFLTTDDRQSPSALPNYEPTPRIHIPGKVHNLLEIIQVDTLIPMNNTHT
KDEVNSYLIPLNANRQNEQVFGTNLFIGDGVFKTTLLGEIVQYYTHWSGSLRFSLMYTGP
ALSSAKLILAYTPPGARGPQDRREAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYTDPDT
YTSAGFLSCWYQTSLILPPETTGQVYLLSFISACPDFKLRLMKDTQTISQTVALTE

Sequence of entity 5 (4), FASTA

>1D3I_5 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4) (chains 4)
GAQVSTQKSGSHENQNILTNGSNQTFTVINYYKDAASTSSAGQSLSMDPSKFTEPVKDLM
LKGAPALN

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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