SAXSdb — 4xt3

▼

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

G-protein coupled receptor homolog US28

Cytomegalovirus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–354	Not recorded	Fractalkine × 1 （P78423） ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 UNL UNKNOWN LIGAND × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；pH 7.4；293 K；PEG 300, HEPES, ammonium phosphate	Resolution 3.80 Å R-free 0.322

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4XT3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4XT1 Structure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1 Deposited 2015-01-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–354（354 aa）	Not recorded	CLR CHOLESTEROL × 2 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 6 UNL UNKNOWN LIGAND × 7 SIN SUCCINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.3；293 K；PEG 300, MES, sodium succinate, polypropylene glycol 400	Resolution 2.89 Å R-free 0.249
7RKF Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state Deposited 2021-07-22	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–354（354 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；1 s blotting before plunging	Resolution 4.00 Å
7RKM Structure of CX3CL1-US28-Gi-scFv16 in C-state Deposited 2021-07-22	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–354（354 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；1 s blotting before plunging	Resolution 3.50 Å
7RKN Structure of CX3CL1-US28-Gi-scFv16 in OC-state Deposited 2021-07-22	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–354（354 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；1 s blotting before plunging	Resolution 3.60 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	US28_HCMVA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–362； UniProt 1–354

Fractalkine

Homo sapiens

UniProt P78423

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 25–101	Fragment：UNP residues 25-101 Non-standard monomer：Yes (specific site not provided by mmCIF)	G-protein coupled receptor homolog US28 × 1 （P69332） ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 UNL UNKNOWN LIGAND × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；pH 7.4；293 K；PEG 300, HEPES, ammonium phosphate	Resolution 3.80 Å R-free 0.322

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4XT3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B2T SOLUTION STRUCTURE OF THE CX3C CHEMOKINE DOMAIN OF FRACTALKINE Deposited 1998-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–100（76 aa） Fragment：CHEMOKINE DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；295.5 K；Pressure 1	Resolution not provided
1F2L CRYSTAL STRUCTURE OF CHEMOKINE DOMAIN OF FRACTALKINE Deposited 2000-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–100（76 aa） Fragment：CHEMOKINE DOMAIN Chain B 25–100（76 aa） Fragment：CHEMOKINE DOMAIN Chain C 25–100（76 aa） Fragment：CHEMOKINE DOMAIN Chain D 25–100（76 aa） Fragment：CHEMOKINE DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；sodium formate, disodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.321
4XT1 Structure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1 Deposited 2015-01-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 25–101（77 aa） Fragment：UNP residues 25-101	Mutation：N9A Non-standard monomer：Yes (specific site not provided by mmCIF)	CLR CHOLESTEROL × 2 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 6 UNL UNKNOWN LIGAND × 7 SIN SUCCINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.3；293 K；PEG 300, MES, sodium succinate, polypropylene glycol 400	Resolution 2.89 Å R-free 0.249
7RKF Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state Deposited 2021-07-22	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 25–101（77 aa） Fragment：UNP residues 25-101	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；1 s blotting before plunging	Resolution 4.00 Å
7RKM Structure of CX3CL1-US28-Gi-scFv16 in C-state Deposited 2021-07-22	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 25–101（77 aa） Fragment：UNP residues 25-101	Non-standard monomer：Yes (specific site not provided by mmCIF)	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；1 s blotting before plunging	Resolution 3.50 Å
7RKN Structure of CX3CL1-US28-Gi-scFv16 in OC-state Deposited 2021-07-22	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 25–101（77 aa） Fragment：UNP residues 25-101	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；1 s blotting before plunging	Resolution 3.60 Å
7XBX Cryo-EM structure of the human chemokine receptor CX3CR1 in complex with CX3CL1 and Gi1 Deposited 2022-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 25–100（76 aa）	Mutation：G35C,I222L,L278C,C323S,M352V Non-standard monomer：Yes (specific site not provided by mmCIF)	CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	X3CL1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–77； UniProt 25–101

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4xt3
Deposition date deposition_date	2015-01-22
Structure title title	Structure of a viral GPCR bound to human chemokine CX3CL1
Keywords keywords	GPCR, chemokine, membrane protein, complex, VIRAL PROTEIN-CYTOKINE complex, VIRAL PROTEIN-SIGNALLING PROTEIN complex; VIRAL PROTEIN/SIGNALLING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

该条目暂无 SAXS 数据。

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

该条目暂无 P(r) 分析数据。

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	G-protein coupled receptor homolog US28
Molecular weight formula_weight	42041.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2774

DYKDDDDAMTPTTTTAELTTEFDYDEDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNFLVIFTITWRRRIQCSGDVYFINLAAADLLFVCTLPLWMQYLLDHNSLASVPCTLLTACFYVAMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQCMTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIAVVLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYVFVGTKFRQELHCLLAEFRQRLFSRDVSWYHSMSFSRRSSPSRRETSSDTLSDEVCRVSQIIP

来源 Source

来源生物 organism	Cytomegalovirus
NCBI Class编号 ncbi_taxonomy_id	10358
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Fractalkine
Molecular weight formula_weight	10013.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QHHGVTKCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQAAALTRNGGSGSGSAAALEVLFQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	627.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	UNKNOWN LIGAND
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4xt3A00
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	4xt3B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	59.900 Å
Unit-cell length b length_b	192.700 Å
Unit-cell length c length_c	94.400 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.801 Å
Low-resolution limit resolution_low	48.920 Å
R factor r_factor	0.2878
R_work r_work	0.2835
R_free r_free	0.3221

Structure of a viral GPCR bound to human chemokine CX3CL1

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

G-protein coupled receptor homolog US28

State in the Current Structure

Other States of the Same Protein in the Database

Fractalkine

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (0)