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1mpv

Structure of bhpBR3, the BAFF-binding loop of BR3 embedded in a beta-hairpin peptide

Method: SOLUTION NMR Dmax: 22.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

BLyS Receptor 3

OrganismNot specified

UniProt Q96RJ3

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 26–31 Fragment：BR3 loop (residues 26-31) Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer SOLUTION NMR NMR measurement conditions：pH 4.5；293 K；Ionic strength (raw mmCIF value) no added salt；Pressure ambient NMR sample composition：2.9 mM bhpBR3 peptide | 92% H2O, 8% D2O, 0.1 mM DSS, pH 4.5 NMR sample composition：2.9 mM bhpBR3 peptide | 100% D2O, 0.1 mM DSS, pH 4.5 Resolution not provided

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 1MPV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1OQE Crystal structure of sTALL-1 with BAFF-R Deposited 2003-03-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 108 PDB declaration: 108-meric
Chain K 16–46（31 aa） Fragment：extracellular domain
Chain L 16–46（31 aa） Fragment：extracellular domain
Chain M 16–46（31 aa） Fragment：extracellular domain
Chain N 16–46（31 aa） Fragment：extracellular domain
Chain O 16–46（31 aa） Fragment：extracellular domain
Chain P 16–46（31 aa） Fragment：extracellular domain
Chain Q 16–46（31 aa） Fragment：extracellular domain
Chain R 16–46（31 aa） Fragment：extracellular domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Resolution 2.50 Å R-free 0.259
1OSX Solution Structure of the Extracellular Domain of BLyS Receptor 3 (BR3) Deposited 2003-03-20 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–61（61 aa） Fragment：extracellular domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5；293 K；Ionic strength (raw mmCIF value) 50 mM NaCl, 25 mM Na2PO4；Pressure ambient
NMR sample composition 1.5 mM BR3 U-15N,25 mM Na2PO4, 50 mM NaCl, 0.1 mM NaN3, 0.1 mM DSS-d10 | 92%H2O/8%D2O
NMR sample composition 1.5 mM BR3 U-15N,13C,25 mM Na2PO4, 50 mM NaCl, 0.1 mM NaN3, 0.1 mM DSS-d10 | 92%H2O/8%D2O
NMR sample composition 1.5 mM BR3 U-15N,13C,25 mM Na2PO4, 50 mM NaCl, 0.1 mM NaN3, 0.1 mM DSS-d10 | 100% D2O
Resolution not provided
2HFG Crystal structure of hBR3 bound to CB3s-Fab Deposited 2006-06-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 7–54（48 aa） Fragment：cysteine rich domain (residues 7-54)
Mutation：V20N, L27P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Drops contained 2.1 microliters protein solution (pH 6.5) and 2.9 microliters of (0.1M citric acid pH 3.0, 24% PEG 3350, and 0.1 M Praseodymium (III) acetate) over a reservoir of 24% PEG 3350. pH of final drop ~4.5.
Resolution 2.61 Å R-free 0.252
4V46 Crystal structure of the BAFF-BAFF-R complex Deposited 2003-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 120 PDB declaration: 120-meric
Chain B0 1–63（63 aa） Fragment：residues 1-63
Chain B1 1–63（63 aa） Fragment：residues 1-63
Chain B2 1–63（63 aa） Fragment：residues 1-63
Chain B3 1–63（63 aa） Fragment：residues 1-63
Chain B4 1–63（63 aa） Fragment：residues 1-63
Chain B5 1–63（63 aa） Fragment：residues 1-63
Chain B6 1–63（63 aa） Fragment：residues 1-63
Chain B7 1–63（63 aa） Fragment：residues 1-63
Chain B8 1–63（63 aa） Fragment：residues 1-63
Chain B9 1–63（63 aa） Fragment：residues 1-63
Chain BA 1–63（63 aa） Fragment：residues 1-63
Chain BB 1–63（63 aa） Fragment：residues 1-63
Chain BC 1–63（63 aa） Fragment：residues 1-63
Chain BD 1–63（63 aa） Fragment：residues 1-63
Chain BE 1–63（63 aa） Fragment：residues 1-63
Chain BF 1–63（63 aa） Fragment：residues 1-63
Chain BG 1–63（63 aa） Fragment：residues 1-63
Chain BH 1–63（63 aa） Fragment：residues 1-63
Chain BI 1–63（63 aa） Fragment：residues 1-63
Chain BJ 1–63（63 aa） Fragment：residues 1-63
Chain BK 1–63（63 aa） Fragment：residues 1-63
Chain BL 1–63（63 aa） Fragment：residues 1-63
Chain BM 1–63（63 aa） Fragment：residues 1-63
Chain BN 1–63（63 aa） Fragment：residues 1-63
Chain BO 1–63（63 aa） Fragment：residues 1-63
Chain BP 1–63（63 aa） Fragment：residues 1-63
Chain BQ 1–63（63 aa） Fragment：residues 1-63
Chain BR 1–63（63 aa） Fragment：residues 1-63
Chain BS 1–63（63 aa） Fragment：residues 1-63
Chain BT 1–63（63 aa） Fragment：residues 1-63
Chain BU 1–63（63 aa） Fragment：residues 1-63
Chain BV 1–63（63 aa） Fragment：residues 1-63
Chain BW 1–63（63 aa） Fragment：residues 1-63
Chain BX 1–63（63 aa） Fragment：residues 1-63
Chain BY 1–63（63 aa） Fragment：residues 1-63
Chain BZ 1–63（63 aa） Fragment：residues 1-63
Chain Ba 1–63（63 aa） Fragment：residues 1-63
Chain Bb 1–63（63 aa） Fragment：residues 1-63
Chain Bc 1–63（63 aa） Fragment：residues 1-63
Chain Bd 1–63（63 aa） Fragment：residues 1-63
Chain Be 1–63（63 aa） Fragment：residues 1-63
Chain Bf 1–63（63 aa） Fragment：residues 1-63
Chain Bg 1–63（63 aa） Fragment：residues 1-63
Chain Bh 1–63（63 aa） Fragment：residues 1-63
Chain Bi 1–63（63 aa） Fragment：residues 1-63
Chain Bj 1–63（63 aa） Fragment：residues 1-63
Chain Bk 1–63（63 aa） Fragment：residues 1-63
Chain Bl 1–63（63 aa） Fragment：residues 1-63
Chain Bm 1–63（63 aa） Fragment：residues 1-63
Chain Bn 1–63（63 aa） Fragment：residues 1-63
Chain Bo 1–63（63 aa） Fragment：residues 1-63
Chain Bp 1–63（63 aa） Fragment：residues 1-63
Chain Bq 1–63（63 aa） Fragment：residues 1-63
Chain Br 1–63（63 aa） Fragment：residues 1-63
Chain Bs 1–63（63 aa） Fragment：residues 1-63
Chain Bt 1–63（63 aa） Fragment：residues 1-63
Chain Bu 1–63（63 aa） Fragment：residues 1-63
Chain Bv 1–63（63 aa） Fragment：residues 1-63
Chain Bw 1–63（63 aa） Fragment：residues 1-63
Chain Bx 1–63（63 aa） Fragment：residues 1-63
Not recorded MG MAGNESIUM ION × 40 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；sodium formate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.30 Å R-free 0.226
8ZUJ Pentagonal cluster of BAFF-BAFFR ectodomain complex Deposited 2024-06-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain A 2–78（77 aa）
Chain B 2–78（77 aa）
Chain C 2–78（77 aa）
Chain G 2–78（77 aa）
Chain H 2–78（77 aa）
Chain I 2–78（77 aa）
Chain M 2–78（77 aa）
Chain N 2–78（77 aa）
Chain O 2–78（77 aa）
Chain S 2–78（77 aa）
Chain T 2–78（77 aa）
Chain U 2–78（77 aa）
Chain Y 2–78（77 aa）
Chain Z 2–78（77 aa）
Chain a 2–78（77 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.58 Å
8ZUK Cluster structure of the BAFF-BAFFR-TRAF3 complex Deposited 2024-06-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain D 1–184（184 aa）
Chain E 1–184（184 aa）
Chain F 1–184（184 aa）
Chain J 1–184（184 aa）
Chain K 1–184（184 aa）
Chain L 1–184（184 aa）
Chain P 1–184（184 aa）
Chain Q 1–184（184 aa）
Chain R 1–184（184 aa）
Chain V 1–184（184 aa）
Chain W 1–184（184 aa）
Chain X 1–184（184 aa）
Chain b 1–184（184 aa）
Chain c 1–184（184 aa）
Chain d 1–184（184 aa）
Chain h 1–184（184 aa）
Chain i 1–184（184 aa）
Chain j 1–184（184 aa）
Chain n 1–184（184 aa）
Chain o 1–184（184 aa）
Chain p 1–184（184 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å

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

View Construct and Data Evidence
UniProt name TR13C_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–10； UniProt 26–31

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 1mpv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1mpv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1mpv
Deposition date deposition_date2002-09-12
Structure title titleStructure of bhpBR3, the BAFF-binding loop of BR3 embedded in a beta-hairpin peptide
Keywords keywordsbeta-hairpin, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier5.79 Å
Radius of gyration Rg (electron density) rg_electron6.51 Å
Forward intensity I(0) i015096300.00
Molecular weight molecular_weight32179.0 kDa
Excluded volume excluded_volume40052 ų
Envelope volume envelope_volume2812 ų
Hydration-shell volume shell_volume3731 ų
Envelope diameter envelope_diameter25.4 Å
Shell Rg shell_rg11.70 Å
Envelope Rg envelope_rg7.88 Å
Shape Rg shape_rg6.37 Å
Total Rg total_rg7.21 Å
Total atoms total_atoms4340
Residues n_residues240
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 dmax22.6 Å
Rg (real space) rg_real5.89 Å
Rg uncertainty (real space) rg_real_error0.32 Å
I(0) (real space) i0_real1.5100e+07
I(0) uncertainty (real space) i0_real_error1.2500e+05
Rg (reciprocal space) rg_reciprocal5.89 Å
I(0) (reciprocal space) i0_reciprocal15100000.0000
Solution quality estimate total_estimate0.7049
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary6.0 Å
Skewness Skewness skewness0.726
Kurtosis Kurtosis kurtosis0.299
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha467.7000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.460; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.295; Smooth: 0.485
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1mpva1
Class classj — Peptides
Fold Fold foldj.98 — Bhpbr3, the Baff-binding loop of br3 embedded in a beta-hairpin peptide
Superfamily Superfamily superfamilyj.98.1 — Bhpbr3, the Baff-binding loop of br3 embedded in a beta-hairpin peptide
Family Family familyj.98.1.1 — Bhpbr3, the Baff-binding loop of br3 embedded in a beta-hairpin peptide
Domain ID domain_idd1mpva2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1mpva3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
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8. Citations (1)

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9. Files and Curves (10)