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2nyz

Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The C- Chemokine XCL1

Method: X-RAY DIFFRACTION Dmax: 110.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hypothetical protein GAMMAHV.M3

Murid herpesvirus 4

UniProt O41925

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 25–406 Chain B； UniProt 25–406 Not recorded Lymphotactin × 2 （P47992） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；10% PEG 8000, 100 mM TRIS, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.60 Å R-free 0.272

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 2NYZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1MKF VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS 68 Deposited 2002-08-29 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 25–406（382 aa）
Chain B 25–406（382 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；293 K；18% PEG4000, 100MM CACL2, 100MM IMIDAZOLE/MALIC ACID PH 5.1, pH 5.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.273
1MKF VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS 68 Deposited 2002-08-29 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 25–406（382 aa）
Chain B 25–406（382 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；293 K；18% PEG4000, 100MM CACL2, 100MM IMIDAZOLE/MALIC ACID PH 5.1, pH 5.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.273
1ML0 VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS68 IN COMPLEX WITH THE P8A VARIANT OF CC-CHEMOKINE MCP-1 Deposited 2002-08-29 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 25–406（382 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；14% PEG4000 200MM, SODIUM ACETATE, 100MM MAGNESIUM CHLORIDE, pH 4.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.282
1ML0 VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS68 IN COMPLEX WITH THE P8A VARIANT OF CC-CHEMOKINE MCP-1 Deposited 2002-08-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 25–406（382 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；14% PEG4000 200MM, SODIUM ACETATE, 100MM MAGNESIUM CHLORIDE, pH 4.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.282
2NZ1 Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The CC-Chemokine CCL2/MCP-1 Deposited 2006-11-22 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 25–406（382 aa）
Chain B 25–406（382 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；12% PEG 4000, 100 mM sodium acetate, 200 mM magnesium chloride, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.300
2NZ1 Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The CC-Chemokine CCL2/MCP-1 Deposited 2006-11-22 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain X 25–406（382 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；12% PEG 4000, 100 mM sodium acetate, 200 mM magnesium chloride, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.300

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O41925_MHV68
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–382； UniProt 25–406 Author chain B； PDBConstruct 1–382； UniProt 25–406

Lymphotactin

OrganismNot specified

UniProt P47992

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain D； UniProt 22–114 Chain E； UniProt 22–114 Not recorded Hypothetical protein GAMMAHV.M3 × 2 （O41925） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；10% PEG 8000, 100 mM TRIS, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.60 Å R-free 0.272

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 2NYZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1J8I Solution Structure of Human Lymphotactin Deposited 2001-05-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–114（93 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；283 K；Ionic strength (raw mmCIF value) 200 mM sodium chloride
NMR sample composition 1.3mM Human Lymphotactin, U-15N,13C; 20 mM phosphate buffer pH 6.0, 200 mM NaCl | 90% H2O/10% D2O
NMR sample composition 1 mM Human Lymphotactin, U-15N; 20 mM phosphate buffer pH 6.0, 200 mM NaCl | 90% H2O/10% D2O
NMR sample composition 1 mM Human Lymphotactin, 20 mM phosphate buffer pH 6.0, 200 mM NaCl | 100% D2O
Resolution not provided
1J9O SOLUTION STRUCTURE OF HUMAN LYMPHOTACTIN Deposited 2001-05-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–114（93 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；283 K；Ionic strength (raw mmCIF value) 200mM NaCl
NMR sample composition 1.3mM human lymphotactin U-15N-13C; 20 mM phosphate buffer, 200mM NaCl | 90% H2O/10% D2O
NMR sample composition 1mM human lymphotactin U-15N; 20 mM phosphate buffer, 200mM NaCl | 90% H2O/10% D2O
NMR sample composition 1mM human lymphotactin; 20 mM phosphate buffer, 200mM NaCl | 100% D2O
Resolution not provided
2HDM Solution structure of V21C/V59C Lymphotactin/XCL1 Deposited 2006-06-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–114（92 aa）
Mutation：V21C, V59C No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure AMBIENT
NMR sample composition 1 mM CC3 hLtn, U-15N, 13C; 20 mM phospate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2JP1 Solution structure of the alternative conformation of XCL1/Lymphotactin Deposited 2007-04-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 22–114（93 aa）
Chain B 22–114（93 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；313 K；Ionic strength (raw mmCIF value) 22；Pressure AMBIENT
NMR sample composition 1.0 mM XCL1 U-15N/13C, 20 mM sodium phosphate, 95% H2O, 5% D2O | 95% H2O/5% D2O
NMR sample composition 0.6 mM XCL1 U-15N/13C, 0.6 mM XCL1 unlabeled, 20 mM sodium phosphate, 95% H2O, 5% D2O | 95% H2O/5% D2O
Resolution not provided
2N54 Solution structure of a disulfide stabilized XCL1 dimer Deposited 2015-07-07 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 22–114（93 aa）
Chain B 22–114（93 aa）
Mutation：A57C, A70C Mutation：A57C, A70C No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；313 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient
NMR sample composition 1 mM [U-99% 13C; U-99% 15N] XCL1, 20 mM potassium phosphate, 0.02 % [U-100% 15N] sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
9AST Cryo-EM structure of XCR1 signaling complex Deposited 2024-02-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain L 22–114（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XCL1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–93； UniProt 22–114 Author chain E； PDBConstruct 1–93； UniProt 22–114

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 2nyz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2nyz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2nyz
Deposition date deposition_date2006-11-21
Structure title titleViral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The C- Chemokine XCL1
Keywords keywordsViral Decoy Receptor, Chemokine, Protein-Protein Complex, VIRAL PROTEIN-CYTOKINE COMPLEX; VIRAL PROTEIN/CYTOKINE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.55 Å
Radius of gyration Rg (electron density) rg_electron30.41 Å
Forward intensity I(0) i0149777000.00
Molecular weight molecular_weight95961.0 kDa
Excluded volume excluded_volume119570 ų
Envelope volume envelope_volume151400 ų
Hydration-shell volume shell_volume40382 ų
Envelope diameter envelope_diameter118.1 Å
Shell Rg shell_rg38.38 Å
Envelope Rg envelope_rg30.60 Å
Shape Rg shape_rg30.41 Å
Total Rg total_rg31.10 Å
Total atoms total_atoms6718
Residues n_residues869
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax110.9 Å
Rg (real space) rg_real31.45 Å
Rg uncertainty (real space) rg_real_error0.89 Å
I(0) (real space) i0_real1.4980e+08
I(0) uncertainty (real space) i0_real_error2.4370e+06
Rg (reciprocal space) rg_reciprocal31.50 Å
I(0) (reciprocal space) i0_reciprocal149800000.0000
Solution quality estimate total_estimate0.6566
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.7 Å
Skewness Skewness skewness0.231
Kurtosis Kurtosis kurtosis-0.435
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha39160000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.785; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.994; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2nyza1
Class classb — All beta proteins
Fold Fold foldb.116 — Viral chemokine binding protein m3
Superfamily Superfamily superfamilyb.116.1 — Viral chemokine binding protein m3
Family Family familyb.116.1.1 — Viral chemokine binding protein m3
Domain ID domain_idd2nyzb1
Class classb — All beta proteins
Fold Fold foldb.116 — Viral chemokine binding protein m3
Superfamily Superfamily superfamilyb.116.1 — Viral chemokine binding protein m3
Family Family familyb.116.1.1 — Viral chemokine binding protein m3

CATH v4.4 (6 domains)

Domain ID domain_id2nyzA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1330 —
Domain ID domain_id2nyzA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1340 — Chemokine-binding protein M3-like
Domain ID domain_id2nyzB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1330 —
Domain ID domain_id2nyzB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1340 — Chemokine-binding protein M3-like
Domain ID domain_id2nyzD00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
Domain ID domain_id2nyzE00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
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8. Citations (1)

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9. Files and Curves (10)