4qzv

Bat-derived coronavirus HKU4 uses MERS-CoV receptor human CD26 for cell entry

Method: X-RAY DIFFRACTION Dmax: 142.3 Å Quality: GOOD

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

Dipeptidyl peptidase 4

Homo sapiens

UniProt P27487

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 4 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 39–766 Not recorded Spike protein S1 × 1 (A3EX94) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;277 K;0.1M sodium citrate, pH 5.5, 15% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.59 Å R-free 0.224
2 Other combination Heteromer Protein × 2 其他Polymer 4 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 39–766 Not recorded Spike protein S1 × 1 (A3EX94) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;277 K;0.1M sodium citrate, pH 5.5, 15% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.59 Å R-free 0.224

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.

113 other PDB entries and 168 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPP4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–728; UniProt 39–766 Author chain C; PDBConstruct 1–728; UniProt 39–766

Spike protein S1

Tylonycteris bat coronavirus HKU4

UniProt A3EX94

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 4 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 372–611 Fragment:receptor binding domain (UNP RESIDUES 372-611) Dipeptidyl peptidase 4 × 1 (P27487) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;277 K;0.1M sodium citrate, pH 5.5, 15% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.59 Å R-free 0.224
2 Other combination Heteromer Protein × 2 其他Polymer 4 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 372–611 Fragment:receptor binding domain (UNP RESIDUES 372-611) Dipeptidyl peptidase 4 × 1 (P27487) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;277 K;0.1M sodium citrate, pH 5.5, 15% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.59 Å R-free 0.224

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPIKE_BCHK4
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–240; UniProt 372–611 Author chain D; PDBConstruct 1–240; UniProt 372–611

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 4qzv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4qzv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4qzv
Deposition date deposition_date2014-07-29
Structure title titleBat-derived coronavirus HKU4 uses MERS-CoV receptor human CD26 for cell entry
Keywords keywords8-BLADED BETA-PROPELLER DOMAIN, ALPHA/BETA HYDROLASE DOMAIN, BLADES IV AND V, CD26 BETA-PROPELLER, HYDROLASE-VIRAL PROTEIN COMPLEX; HYDROLASE/VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier44.69
Radius of gyration Rg (electron density) rg_electron44.25
Forward intensity I(0) i0687337000.00
Molecular weight molecular_weight218680.0 kDa
Excluded volume excluded_volume273740 ų
Envelope volume envelope_volume375310 ų
Hydration-shell volume shell_volume68742 ų
Envelope diameter envelope_diameter143.6
Shell Rg shell_rg50.90
Envelope Rg envelope_rg43.83
Shape Rg shape_rg44.17
Total Rg total_rg44.82
Total atoms total_atoms15424
Residues n_residues1870
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 dmax142.3
Rg (real space) rg_real44.61
Rg uncertainty (real space) rg_real_error1.43
I(0) (real space) i0_real6.8730e+08
I(0) uncertainty (real space) i0_real_error1.2490e+07
Rg (reciprocal space) rg_reciprocal44.69
I(0) (reciprocal space) i0_reciprocal687400000.0000
Solution quality estimate total_estimate0.8784
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.8
Skewness Skewness skewness0.201
Kurtosis Kurtosis kurtosis-0.650
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha72720000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.607

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4qzva1
Class classb — All beta proteins
Fold Fold foldb.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamilyb.70.3 — DPP6 N-terminal domain-like
Family Family familyb.70.3.1 — DPP6 N-terminal domain-like
Domain ID domain_idd4qzva2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.0 — automated matches
Domain ID domain_idd4qzvc1
Class classb — All beta proteins
Fold Fold foldb.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamilyb.70.3 — DPP6 N-terminal domain-like
Family Family familyb.70.3.1 — DPP6 N-terminal domain-like
Domain ID domain_idd4qzvc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id4qzvA01
Class class2 — Mainly Beta
Architecture architecture140 — 8 Propeller
Topology topology10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
Domain ID domain_id4qzvA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id4qzvB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1840 — Spike protein, C-terminal core receptor binding subdomain
Domain ID domain_id4qzvB02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology210 — ubp-family deubiquitinating enzyme fold
Homologous superfamily homologous superfamily30
Domain ID domain_id4qzvC01
Class class2 — Mainly Beta
Architecture architecture140 — 8 Propeller
Topology topology10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
Domain ID domain_id4qzvC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id4qzvD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1840 — Spike protein, C-terminal core receptor binding subdomain
Domain ID domain_id4qzvD02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology210 — ubp-family deubiquitinating enzyme fold
Homologous superfamily homologous superfamily30

8. Citations (1)

9. Files and Curves (10)