7rkf

Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state

Method: ELECTRON MICROSCOPY Dmax: 152.4 Å Quality: GOOD

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

Guanine nucleotide-binding protein subunit alpha-11

Homo sapiens

UniProt P29992

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 25–359 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Antibody fragment scFv16 × 1 Fractalkine × 1 (P78423) G-protein coupled receptor homolog US28 × 1 (P69332) 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

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.

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNA11_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 18–352; UniProt 25–359

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Homo sapiens

UniProt P62873

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Guanine nucleotide-binding protein subunit alpha-11 × 1 (P29992) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Antibody fragment scFv16 × 1 Fractalkine × 1 (P78423) G-protein coupled receptor homolog US28 × 1 (P69332) 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

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.

1260 other PDB entries and 1263 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 7–345; UniProt 2–340

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Homo sapiens

UniProt P59768

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 2–68 Not recorded Guanine nucleotide-binding protein subunit alpha-11 × 1 (P29992) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Antibody fragment scFv16 × 1 Fractalkine × 1 (P78423) G-protein coupled receptor homolog US28 × 1 (P69332) 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

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.

1233 other PDB entries and 1236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–67; UniProt 2–68

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain L; UniProt 25–101 Fragment:UNP residues 25-101 Non-standard monomer:Yes (specific site not provided by mmCIF) Guanine nucleotide-binding protein subunit alpha-11 × 1 (P29992) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Antibody fragment scFv16 × 1 G-protein coupled receptor homolog US28 × 1 (P69332) 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

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.

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 5
Chains and sequence ranges Author chain L; PDBConstruct 1–77; UniProt 25–101

G-protein coupled receptor homolog US28

Human 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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain R; UniProt 1–354 Not recorded Guanine nucleotide-binding protein subunit alpha-11 × 1 (P29992) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Antibody fragment scFv16 × 1 Fractalkine × 1 (P78423) 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

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.

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 6
Chains and sequence ranges Author chain R; PDBConstruct 9–362; UniProt 1–354

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

SAXS profile for 7rkf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7rkf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7rkf
Deposition date deposition_date2021-07-22
Structure title titleStructure of CX3CL1-US28-G11iN18-scFv16 in TL-state
Keywords keywordsViral GPCR, HCMV, cytomegalovirus, G protein complex, GDP-bound state, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier43.35
Radius of gyration Rg (electron density) rg_electron43.31
Forward intensity I(0) i0332843000.00
Molecular weight molecular_weight150240.0 kDa
Excluded volume excluded_volume188630 ų
Envelope volume envelope_volume278020 ų
Hydration-shell volume shell_volume56296 ų
Envelope diameter envelope_diameter163.6
Shell Rg shell_rg44.98
Envelope Rg envelope_rg43.74
Shape Rg shape_rg43.29
Total Rg total_rg43.46
Total atoms total_atoms10563
Residues n_residues1333
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax152.4
Rg (real space) rg_real43.53
Rg uncertainty (real space) rg_real_error1.75
I(0) (real space) i0_real3.3280e+08
I(0) uncertainty (real space) i0_real_error6.4270e+06
Rg (reciprocal space) rg_reciprocal43.35
I(0) (reciprocal space) i0_reciprocal332800000.0000
Solution quality estimate total_estimate0.8608
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.8
Skewness Skewness skewness0.452
Kurtosis Kurtosis kurtosis-0.168
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44330000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.823

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7rkfA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology400 — GI Alpha 1, domain 2-like
Homologous superfamily homologous superfamily10 — GI Alpha 1, domain 2-like
Domain ID domain_id7rkfB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id7rkfD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7rkfD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)