SAXSdb — 5w0p

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

Endolysin,Rhodopsin,S-arrestin

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A097J792_BPT4
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–160； UniProt 2–161 Author chain B； PDBConstruct 1–160； UniProt 2–161 Author chain C； PDBConstruct 1–160； UniProt 2–161 Author chain D； PDBConstruct 1–160； UniProt 2–161

Endolysin,Rhodopsin,S-arrestin

Mus musculus

UniProt P08100

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OPSD_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 161–508； UniProt 1–348 Author chain B； PDBConstruct 161–508； UniProt 1–348 Author chain C； PDBConstruct 161–508； UniProt 1–348 Author chain D； PDBConstruct 161–508； UniProt 1–348

Endolysin,Rhodopsin,S-arrestin

Mus musculus

UniProt P20443

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARRS_MOUSE
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 524–906； UniProt 10–392 Author chain B； PDBConstruct 524–906； UniProt 10–392 Author chain C； PDBConstruct 524–906； UniProt 10–392 Author chain D； PDBConstruct 524–906； UniProt 10–392

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	5w0p
Deposition date deposition_date	2017-05-31
Structure title title	Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser
Keywords keywords	rhodopsin, GPCR, arrestin, GRK, phosphorylation codes, membrane proteins, SIGNALING PROTEIN; SIGNALING 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.

5w0p__assembly_1__model_1

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

Download this curve (.dat)

5w0p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5w0p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.76 Å
Rg (electron density)	40.44 Å
Total Rg	40.62 Å
Atom count	6730
Residues	847
Excluded volume	121490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5w0p__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5w0p__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5w0p__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5w0p__assembly_4__model_1`	monomeric （1）	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	Endolysin,Rhodopsin,S-arrestin
Molecular weight formula_weight	101023.0 kDa
EC 编号 ec_number	3.2.1.17
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	25976

NIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYMCGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLQGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIYVIAFLICWVPYASVAFYIFTHQGSCFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPAGSAGSAGSAGSAGSASHVIFKKVSRDKSVTIYLGKRDYVDHVSQVEPVDGVVLVDPELVKGKKVYVTLTCAFRYGQEDIDVMGLTFRRDLYFSRVQVYPPVGAMSVLTQLQESLLKKLGDNTYPFLLTFPDYLPCSVMLQPAPQDVGKSCGVDFEVKAFASDITDPEEDKIPKKSSVRLLIRKVQHAPPEMGPQPSAEASWQFFMSDKPLNLSVSLSKEIYFHGEPIPVTVTVTNNTDKVVKKIKVSVEQIANVVLYSSDYYVKPVASEETQEKVQPNSTLTKTLVLVPLLANNRERRGIALDGKIKHEDTNLASSTIIKEGIDRTVMGILVSYHIKVKLTVSGFLGELTSSEVATEVPFRLMHPQPEDPAKESVQDENAAAEEFARQNLKDTGENTE

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Endolysin,Rhodopsin,S-arrestin
Molecular weight formula_weight	100943.1 kDa
EC 编号 ec_number	3.2.1.17
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

NIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYMCGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLQGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIYVIAFLICWVPYASVAFYIFTHQGSCFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPAGSAGSAGSAGSAGSASHVIFKKVSRDKSVTIYLGKRDYVDHVSQVEPVDGVVLVDPELVKGKKVYVTLTCAFRYGQEDIDVMGLTFRRDLYFSRVQVYPPVGAMSVLTQLQESLLKKLGDNTYPFLLTFPDYLPCSVMLQPAPQDVGKSCGVDFEVKAFASDITDPEEDKIPKKSSVRLLIRKVQHAPPEMGPQPSAEASWQFFMSDKPLNLSVSLSKEIYFHGEPIPVTVTVTNNTDKVVKKIKVSVEQIANVVLYSSDYYVKPVASEETQEKVQPNSTLTKTLVLVPLLANNRERRGIALDGKIKHEDTNLASSTIIKEGIDRTVMGILVSYHIKVKLTVSGFLGELTSSEVATEVPFRLMHPQPEDPAKESVQDENAAAEEFARQNLKDTGENTE

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5w0pA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	5w0pA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily	10 — Rhodopsin 7-helix transmembrane proteins

Domain ID domain_id	5w0pA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	840 —

Domain ID domain_id	5w0pA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	640 —

Domain ID domain_id	5w0pC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	5w0pC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily	10 — Rhodopsin 7-helix transmembrane proteins

Domain ID domain_id	5w0pC03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	840 —

Domain ID domain_id	5w0pC04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	640 —

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Unit-cell length a length_a	109.240 Å
Unit-cell length b length_b	109.240 Å
Unit-cell length c length_c	452.640 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.013 Å
Low-resolution limit resolution_low	30.030 Å
R factor r_factor	0.2369
R_work r_work	0.2343
R_free r_free	0.2722

Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser

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

Endolysin,Rhodopsin,S-arrestin

State in the Current Structure

Other States of the Same Protein in the Database

Endolysin,Rhodopsin,S-arrestin

State in the Current Structure

Other States of the Same Protein in the Database

Endolysin,Rhodopsin,S-arrestin

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

5w0p__assembly_1__model_1

5w0p__assembly_1__model_1 | I(q)

5w0p__assembly_1__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 branched

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser

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

Endolysin,Rhodopsin,S-arrestin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Endolysin,Rhodopsin,S-arrestin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Endolysin,Rhodopsin,S-arrestin

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

5w0p__assembly_1__model_1

5w0p__assembly_1__model_1 | I(q)

5w0p__assembly_1__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 branched

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)