7o7f

Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist

Method: ELECTRON MICROSCOPY Dmax: 140.8 Å Quality: REASONABLE

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

Guanine nucleotide-binding protein G(i) subunit alpha-1

Homo sapiens

UniProt P63096

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 1–354 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) C-C chemokine receptor type 5 × 1 (P51681) Guanine nucleotide-binding protein G(T) subunit gamma-T1 × 1 (P02698) C-C motif chemokine 5 × 1 (P13501) Fab antibody fragment heavy chain × 1 Fab antibody fragment light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.15 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.

573 other PDB entries and 591 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–354; UniProt 1–354

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

OrganismNot specified

UniProt P62871

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain B; UniProt 1–340 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) C-C chemokine receptor type 5 × 1 (P51681) Guanine nucleotide-binding protein G(T) subunit gamma-T1 × 1 (P02698) C-C motif chemokine 5 × 1 (P13501) Fab antibody fragment heavy chain × 1 Fab antibody fragment light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.15 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.

72 other PDB entries and 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–340; UniProt 1–340

C-C chemokine receptor type 5

Homo sapiens

UniProt P51681

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain C; UniProt 1–352 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Guanine nucleotide-binding protein G(T) subunit gamma-T1 × 1 (P02698) C-C motif chemokine 5 × 1 (P13501) Fab antibody fragment heavy chain × 1 Fab antibody fragment light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.15 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.

19 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CCR5_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–352; UniProt 1–352

Guanine nucleotide-binding protein G(T) subunit gamma-T1

OrganismNot specified

UniProt P02698

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain G; UniProt 1–74 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) C-C chemokine receptor type 5 × 1 (P51681) C-C motif chemokine 5 × 1 (P13501) Fab antibody fragment heavy chain × 1 Fab antibody fragment light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.15 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.

16 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG1_BOVIN
Isoform
PDB entities 4
Chains and sequence ranges Author chain G; PDBConstruct 1–74; UniProt 1–74

C-C motif chemokine 5

Homo sapiens

UniProt P13501

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain I; UniProt 23–91 Non-standard monomer:Yes (specific site not provided by mmCIF) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) C-C chemokine receptor type 5 × 1 (P51681) Guanine nucleotide-binding protein G(T) subunit gamma-T1 × 1 (P02698) Fab antibody fragment heavy chain × 1 Fab antibody fragment light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.15 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.

22 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CCL5_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain I; PDBConstruct 1–69; UniProt 23–91

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 7o7f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7o7f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7o7f
Deposition date deposition_date2021-04-13
Structure title titleStructural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist
Keywords keywords;G protein-coupled receptor (GPCR); CCR5; CCL5/RANTES; HIV entry; AIDS; membrane protein structure;, MEMBRANE PROTEIN, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier45.68
Radius of gyration Rg (electron density) rg_electron45.58
Forward intensity I(0) i0367830000.00
Molecular weight molecular_weight158730.0 kDa
Excluded volume excluded_volume199150 ų
Envelope volume envelope_volume275710 ų
Hydration-shell volume shell_volume53002 ų
Envelope diameter envelope_diameter148.1
Shell Rg shell_rg46.27
Envelope Rg envelope_rg45.63
Shape Rg shape_rg45.57
Total Rg total_rg45.65
Total atoms total_atoms11155
Residues n_residues1419
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 dmax140.8
Rg (real space) rg_real46.92
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real3.6190e+08
I(0) uncertainty (real space) i0_real_error5.2350e+06
Rg (reciprocal space) rg_reciprocal45.68
I(0) (reciprocal space) i0_reciprocal367800000.0000
Solution quality estimate total_estimate0.6602
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.2
Skewness Skewness skewness0.311
Kurtosis Kurtosis kurtosis-0.683
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha2.8180
Highest regularization parameter α highest_alpha23550000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.984; Stabil: 0.904; Sysdev: 0.000; Positv: 1.000; Valcen: 0.902; Smooth: 0.030

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd7o7fb_
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.4 — WD40 repeat-like
Family Family familyb.69.4.1 — WD40-repeat
Domain ID domain_idd7o7ff1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd7o7ff2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd7o7fg_
Class classa — All alpha proteins
Fold Fold folda.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamilya.137.3 — Transducin (heterotrimeric G protein), gamma chain
Family Family familya.137.3.1 — Transducin (heterotrimeric G protein), gamma chain
Domain ID domain_idd7o7fh_
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_idd7o7fi_
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

CATH v4.4 (5 domains)

Domain ID domain_id7o7fB01
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_id7o7fF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7o7fF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7o7fH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7o7fH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)