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4xt1

Structure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

G-protein coupled receptor homolog US28

Cytomegalovirus

UniProt P69332

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–354 Not recorded Fractalkine × 1 （P78423） nanobody 7 × 1 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

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 4XT1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4XT3 Structure of a 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 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–354（354 aa）
Not recorded 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
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 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 25–101 Fragment：UNP residues 25-101 Mutation：N9A Non-standard monomer：Yes (specific site not provided by mmCIF) G-protein coupled receptor homolog US28 × 1 （P69332） nanobody 7 × 1 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

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 4XT1 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
4XT3 Structure of a 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 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 25–101（77 aa） Fragment：UNP residues 25-101
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
7RKF Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state Deposited 2021-07-22 Different mutation/modification 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 mutation/modification 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 mutation/modification 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.

SAXS scattering curve SAXS Profile

暂无 SAXS 图

P(r) Distance Distribution P(r) Distribution

暂无 P(r) 图
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4xt1
Deposition date deposition_date2015-01-22
Structure title titleStructure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1
Keywords keywordsGPCR, chemokine, membrane protein, complex, VIRAL PROTEIN-SIGNALLING PROTEIN complex; VIRAL PROTEIN/SIGNALLING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

该条目暂无 SAXS 数据。

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

该条目暂无 P(r) 分析数据。

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd4xt1b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.9 — IL8-like
Superfamily Superfamily superfamilyd.9.1 — Interleukin 8-like chemokines
Family Family familyd.9.1.1 — Interleukin 8-like chemokines
Domain ID domain_idd4xt1c1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd4xt1c2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id4xt1A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins
Domain ID domain_id4xt1B00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
Domain ID domain_id4xt1C00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (0)