8u4q

Structure of REGN7663 Fab-bound CXCR4/Gi complex

Method: ELECTRON MICROSCOPY Dmax: 180.2 Å Quality: REASONABLE

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

C-X-C chemokine receptor type 4

Homo sapiens

UniProt P61073

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 2–352 Not recorded REGN7663 Fab light chain × 1 REGN7663 Fab heavy chain × 1 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 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.36 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.

32 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CXCR4_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain R; PDBConstruct 20–370; UniProt 2–352

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 2–354 Not recorded REGN7663 Fab light chain × 1 REGN7663 Fab heavy chain × 1 C-X-C chemokine receptor type 4 × 1 (P61073) 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) CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.36 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 4
Chains and sequence ranges Author chain A; PDBConstruct 13–365; UniProt 2–354

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 REGN7663 Fab light chain × 1 REGN7663 Fab heavy chain × 1 C-X-C chemokine receptor type 4 × 1 (P61073) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.36 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 5
Chains and sequence ranges Author chain B; PDBConstruct 12–350; 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 1–71 Not recorded REGN7663 Fab light chain × 1 REGN7663 Fab heavy chain × 1 C-X-C chemokine receptor type 4 × 1 (P61073) 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 (P62873) CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.36 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 6
Chains and sequence ranges Author chain C; PDBConstruct 1–71; UniProt 1–71

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 8u4q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8u4q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8u4q
Deposition date deposition_date2023-09-11
Structure title titleStructure of REGN7663 Fab-bound CXCR4/Gi complex
Keywords keywordsGPCR, chemokine receptor, antibody, Fab, SIGNALING PROTEIN-IMMUNE SYSTEM complex; SIGNALING PROTEIN/IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier54.55
Radius of gyration Rg (electron density) rg_electron54.83
Forward intensity I(0) i0314216000.00
Molecular weight molecular_weight148020.0 kDa
Excluded volume excluded_volume185750 ų
Envelope volume envelope_volume280110 ų
Hydration-shell volume shell_volume47440 ų
Envelope diameter envelope_diameter193.0
Shell Rg shell_rg48.40
Envelope Rg envelope_rg55.03
Shape Rg shape_rg54.78
Total Rg total_rg54.75
Total atoms total_atoms10409
Residues n_residues1339
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 dmax180.2
Rg (real space) rg_real55.35
Rg uncertainty (real space) rg_real_error2.54
I(0) (real space) i0_real3.1420e+08
I(0) uncertainty (real space) i0_real_error6.4140e+06
Rg (reciprocal space) rg_reciprocal53.85
I(0) (reciprocal space) i0_reciprocal313500000.0000
Solution quality estimate total_estimate0.6721
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary174.0
Skewness Skewness skewness0.532
Kurtosis Kurtosis kurtosis-0.695
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14760000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.450; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.374; Smooth: 0.010

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (2)

9. Files and Curves (10)