SAXSdb — 1d3e

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1)

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 300	PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 60 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2) × 60 （Q82122） PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3) × 60 （Q82122） PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4) × 60 （Q82122）	Consistent with protein count
2	Insufficient information	Heteromer	Protein 5	PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 1 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2) × 1 （Q82122） PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3) × 1 （Q82122） PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4) × 1 （Q82122）	Consistent with protein count
3	Insufficient information	Heteromer	Protein 25	PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 5 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2) × 5 （Q82122） PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3) × 5 （Q82122） PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4) × 5 （Q82122）	Consistent with protein count
4	Insufficient information	Heteromer	Protein 30	PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 6 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2) × 6 （Q82122） PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3) × 6 （Q82122） PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4) × 6 （Q82122）	Consistent with protein count
5	Insufficient information	Heteromer	Protein 5	PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 1 PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2) × 1 （Q82122） PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3) × 1 （Q82122） PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4) × 1 （Q82122）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ICAM1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 1； PDBConstruct 1–185； UniProt 28–212

PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1)

OrganismNot specified

UniProt Q82122

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 300	PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 60	Consistent with protein count
2	Insufficient information	Heteromer	Protein 5	PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 1	Consistent with protein count
3	Insufficient information	Heteromer	Protein 25	PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 5	Consistent with protein count
4	Insufficient information	Heteromer	Protein 30	PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 6	Consistent with protein count
5	Insufficient information	Heteromer	Protein 5	PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_HRV16
Isoform	—
PDB entities	2, 3, 4, 5
Chains and sequence ranges	Author chain 1； PDBConstruct 1–285； UniProt 573–852 Author chain 2； PDBConstruct 1–252； UniProt 78–329 Author chain 3； PDBConstruct 1–238； UniProt 330–567 Author chain 4； PDBConstruct 1–68； UniProt 1–68

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d3e
Deposition date deposition_date	1999-09-29
Structure title title	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
Keywords keywords	;HUMAN RHINOVIRUS, HRV16, ICAM-1, FITTING OF X-RAY STRUCTURES INTO CRYO-EM RECONSTRUCTIONS, COMMON COLD, VIRUS UNCOATING, VIRUS/ VIRAL PROTEIN, RHINOVIRUS-RECEPTOR COMPLEX, Icosahedral virus, Virus-Receptor COMPLEX ;; Virus/Receptor
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1d3e__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1d3e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1d3e__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	0.00 Å
Rg (electron density)	142.10 Å
Total Rg	142.10 Å
Atom count	0
Residues	0
Excluded volume	8051900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1d3e__assembly_1__model_1`	300-MERIC （300）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1d3e__assembly_2__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`1d3e__assembly_3__model_1`	25-meric （25）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`1d3e__assembly_4__model_1`	30-meric （30）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`1d3e__assembly_5__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PROTEIN (INTERCELLULAR ADHESION MOLECULE-1)
Molecular weight formula_weight	20438.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I
Atom count atom_count	989

QTSVSPSKVILPRGGSVLVTCSTSCDQPKLLGIETPLPKKELLLPGNNRKVYELSNVQEDSQPMCYSNCPDGQSTAKTFLTVYWTPERVELAPLPSWQPVGKNLTLRCQVEGGAPRANLTVVLLRGEKELKREPAVGEPAEVTTTVLVRRDHHGANFSCRTELDLRPQGLELFENTSAPYQLQTF

Entity 2 Entity 2 polymer

Description description	PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1)
Molecular weight formula_weight	32314.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1

APVAAYVDEVLNEVLVVPNINQSHPTTSNAAPVLDAAETGHTNKIQPEDTIETRYVQSSQTLDEMSVESFLGRSGCIHESVLDIVDNYNDQSFTKWNINLQEMAQIRRKFEMFTYARFDSEITMVPSVAAKDGHIGHIVMQYMYVPPGAPIPTTRDDYAWQSGTNASVFWQHGQPFPRFSLPFLSIASAYYMFYDGYDGDTYKSRYGTVVTNDMGTLCSRIVTSEQLHKVKVVTRIYHKAKHTKAWCPRPPRAVQYSHTHTTNYKLSSEVHNDVAIRPRTNLTTV

Entity 3 Entity 3 polymer

Description description	PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2)
Molecular weight formula_weight	27910.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

SDRIIQITRGDSTITSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSSNRFYTLDSKMWNSTSKGWWWKLPDALKDMGIFGENMFYHFLGRSGYTVHVQCNASKFHQGTLLVVMIPEHQLATVNKGNVNAGYKYTHPGEAGREVGTAAAAEKQPSDDNWLNFDGTLLGNLLIFPHQFINLRSNNSATLIVPYVNAVPMDSMVRHNNWSLVIIPVCQLQSNNISNIVPITVSISPMCAEFSGARAKTVVQ

Entity 4 Entity 4 polymer

Description description	PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3)
Molecular weight formula_weight	26314.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3

GLPVYVTPGSGQFMTTDDMQSPCALPWYHPTKEIFIPGEVKNLIEMCQVDTLIPINSTQSNIGNVSMYTVTLSPQTKLAEEIFAIKVDIASHPLATTLIGEIASYFTHWTGSLRFSFMFCGTANTTLKVLLAYTPPGIGKPRSRKEAMLGTHVVWDVGLQSTVSLVVPWISASQYRFTTPDTYSSAGYITCWYQTNFVVPPNTPNTAEMLCFVSGCKDFCLRMARDTDLHKQTGPITQ

Entity 5 Entity 5 polymer

Description description	PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4)
Molecular weight formula_weight	7374.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4

GAQVSRQNVGTHSTQNMVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1d3e1_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1d3e2_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1d3e3_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1d3e4_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1d3ei_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	28.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	28.00 Å
Resolution测定Method resolution_method	;COMMON-LINES AND POLAR-FOURIER-TRANSFORM FULLER ET AL. 1996, J.STRUC.BIOL.c 116, 48-55; BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130 ;
颗粒数 num_particles	44

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1)

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1d3e__assembly_1__model_1

1d3e__assembly_1__model_1 | I(q)

1d3e__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

7. Citations (5)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1d3e__assembly_1__model_1

1d3e__assembly_1__model_1 | I(q)

1d3e__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

7. Citations (5)