SAXSdb — 1m9e

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

Cyclophilin A

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	HIV-1 Capsid × 1 （Q72497） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	HIV-1 Capsid × 1 （Q72497） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPIA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–164； UniProt 1–163 Author chain B； PDBConstruct 1–164； UniProt 1–163

HIV-1 Capsid

Human immunodeficiency virus 1

UniProt Q72497

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cyclophilin A × 1 （P62937） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cyclophilin A × 1 （P62937） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q72497_9HIV1
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–146； UniProt 133–278 Author chain D； PDBConstruct 1–146； UniProt 133–278

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	1m9e
Deposition date deposition_date	2002-07-28
Structure title title	X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A Complex.
Keywords keywords	CAPSID, HIV-1, CYCLOPHILIN A, ISOMERASE, ROTAMASE, Isomerase-Viral protein COMPLEX; Isomerase/Viral protein
Experimental Method method	X-RAY DIFFRACTION

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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.

1m9e__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1m9e__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1m9e__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.46 Å
Rg (electron density)	24.35 Å
Total Rg	25.10 Å
Atom count	2373
Residues	308
Excluded volume	42181 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1m9e__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1m9e__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cyclophilin A
Molecular weight formula_weight	17907.4 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5057

MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	HIV-1 Capsid
Molecular weight formula_weight	16137.5 kDa
Mutation mutation	H87A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVAAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYS

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	380

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1m9ea_
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

Domain ID domain_id	d1m9eb_
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

Domain ID domain_id	d1m9ec_
Class class	a — All alpha proteins
Fold Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

Domain ID domain_id	d1m9ed_
Class class	a — All alpha proteins
Fold Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

CATH v4.4 (4 domains)

Domain ID domain_id	1m9eA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

Domain ID domain_id	1m9eB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

Domain ID domain_id	1m9eC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

Domain ID domain_id	1m9eD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

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Unit-cell length a length_a	38.289 Å
Unit-cell length b length_b	110.989 Å
Unit-cell length c length_c	67.685 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.720 Å
Low-resolution limit resolution_low	25.730 Å
R factor r_factor	0.1780
R_work r_work	0.1729
R_free r_free	0.2257

X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A Complex.

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

Cyclophilin A

State in the Current Structure

Other States of the Same Protein in the Database

HIV-1 Capsid

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

1m9e__assembly_2__model_1

1m9e__assembly_2__model_1 | I(q)

1m9e__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A Complex.

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

Cyclophilin A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HIV-1 Capsid

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

1m9e__assembly_2__model_1

1m9e__assembly_2__model_1 | I(q)

1m9e__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)