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1mwn

Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12

Method: SOLUTION NMR Dmax: 60.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

S-100 protein, beta chain

Rattus norvegicus

UniProt P04631

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 0–91 Chain B； UniProt 0–91 Not recorded F-actin capping protein alpha-1 subunit × 2 （P52907） CA CALCIUM ION × 4 SOLUTION NMR NMR measurement conditions：pH 6.5；310 K；Ionic strength (raw mmCIF value) 25 mM；Pressure ambient NMR sample composition：2.2 mM S100B (subunit concentration), 5.2 mM CaCl2, 2.6 mM TRTK-12 peptide, 10 mM tris-d11, 15 mM NaCl, 0.1 mM EDTA, 5 mM DTT, 0.35 mM NaN3 | 95% H2O/5% D2O 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 1MWN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B4C SOLUTION STRUCTURE OF RAT APO-S100B USING DIPOLAR COUPLINGS Deposited 1998-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–91（91 aa）
Chain B 1–91（91 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 25mM；Pressure 1
Resolution not provided
1DT7 SOLUTION STRUCTURE OF THE C-TERMINAL NEGATIVE REGULATORY DOMAIN OF P53 IN A COMPLEX WITH CA2+-BOUND S100B(BB) Deposited 2000-01-11 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–92（92 aa） Fragment：BETA CHAIN
Chain B 1–92（92 aa） Fragment：BETA CHAIN
Not recorded CA CALCIUM ION × 4 SOLUTION NMR
NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 25 mM；Pressure ambient
NMR sample composition 3-6 mM S100 (subunit concentration), 0.1 mM EDTA, 0.34 mM NaN3, 5 mM DTT, 17 mM NaCl, 10 mM d11-tris-HCl, 7% D2O, 6-13 mM CaCl2, 4.8-10 mM p53 peptide | 7% D2O, 93% H2O
Resolution not provided
1QLK SOLUTION STRUCTURE OF CA(2+)-LOADED RAT S100B (BETABETA) NMR, 20 STRUCTURES Deposited 1997-09-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–91（91 aa） Fragment：SUBUNITS A AND B
Chain B 1–91（91 aa） Fragment：SUBUNITS A AND B
Not recorded CA CALCIUM ION × 4 SOLUTION NMR
NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 22mM；Pressure ATMOSPHERIC
NMR sample composition WATER
Resolution not provided
1SYM 3-D SOLUTION STRUCTURE OF REDUCED APO-S100B FROM RAT, NMR, 20 STRUCTURES Deposited 1996-05-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–91（91 aa）
Chain B 1–91（91 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1XYD NMR Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures Deposited 2004-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 0–91（92 aa）
Chain B 0–91（92 aa）
Not recorded CA CALCIUM ION × 4 ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.2；310.15 K；Pressure ambient
NMR sample composition 3 mM 15N S100B (monomer concentration), 3 mM Zinc acetate, 10 mM CaCl2, 0.34 mM NaN3, 15 mM NaCl, <0.07 mM DTT, 10 mM TES, 10% D2O
NMR sample composition 3 mM 15N,13C S100B (monomer concentration), 3 mM Zinc acetate, 10 mM CaCl2, 0.34 mM NaN3, 15 mM NaCl, <0.07 mM DTT, 10 mM TES, 10% D2O
NMR sample composition 1 mM 15N S100B (monomer concentration), 1 mM Zinc acetate, 3.3 mM CaCl2, 0.34 mM NaN3, 15 mM NaCl, <0.07 mM DTT, 10 mM TES, 10% D2O
Resolution not provided
2K7O Ca2+-S100B, refined with RDCs Deposited 2008-08-17 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–92（91 aa）
Chain B 2–92（91 aa）
Not recorded CA CALCIUM ION × 4 SOLUTION NMR
NMR measurement conditions pH 6.7；310 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 400 uM [U-15N] S100B, 10 mM CaCl2, 25 mM NaCl, 10 mM [U-99% 2H] MES, pH 6.7, 10 mM DTT, .1 mM NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

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

View Construct and Data Evidence
UniProt name S100B_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–92； UniProt 0–91 Author chain B； PDBConstruct 1–92； UniProt 0–91

F-actin capping protein alpha-1 subunit

OrganismNot specified

UniProt P52907

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 X； UniProt 265–276 Chain Y； UniProt 265–276 Fragment：Residues 265-276 S-100 protein, beta chain × 2 （P04631） CA CALCIUM ION × 4 SOLUTION NMR NMR measurement conditions：pH 6.5；310 K；Ionic strength (raw mmCIF value) 25 mM；Pressure ambient NMR sample composition：2.2 mM S100B (subunit concentration), 5.2 mM CaCl2, 2.6 mM TRTK-12 peptide, 10 mM tris-d11, 15 mM NaCl, 0.1 mM EDTA, 5 mM DTT, 0.35 mM NaN3 | 95% H2O/5% D2O 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 1MWN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1MQ1 Ca2+-S100B-TRTK-12 complex Deposited 2002-09-13 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 265–276（12 aa） Fragment：TRTK-12 peptide, RESIDUES 265-276
Chain D 265–276（12 aa） Fragment：TRTK-12 peptide, RESIDUES 265-276
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.05；308 K；Ionic strength (raw mmCIF value) 35 mM KCl；Pressure ambient
NMR sample composition U-13C, U-15N S100B (1.0 mM) unlabelled TRTK-12 (1.2 mM) 3 mM CaCl2 | 90% H20, 10% D20
NMR sample composition U-2H, U-15N S100B (0.35 mM) unlabelled TRTK-12 (0.80 mM) 1 mM CaCl2 | 90% H20, 10% D20
NMR sample composition U-13C, U-15N S100B (1.0 mM) 13C-acetyl, 13C-Ile TRTK-12 (1.2 mM) 3 mM CaCl2 | 90% H20, 10% D20
NMR sample composition U-13C/U-12C S100B heterodimer (1.0mM) Unlabelled TRTK-12 (1.2 mM) 3 mM CaCl2 | 90% H20, 10% D20
Resolution not provided
7T5Q Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation Deposited 2021-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: decameric
Chain I 1–280（280 aa）
Not recorded MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 3 seconds with Whatman 41 filter paper and manually plunged using a Leica EM CPC manual plunger.
Resolution 3.40 Å
8F8Q Cryo-EM structure of the CapZ-capped barbed end of F-actin Deposited 2022-11-22 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 × 8 PDB declaration: octameric
Chain G 1–286（286 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 0 Blot time 2.5 s
Resolution 2.79 Å
9B7J Cryo-EM structure of human dynactin complex bound to Chlamydia effector Dre1 Deposited 2024-03-27 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 × 25 PDB declaration: 25-meric
Chain N 1–286（286 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.49 Å
9B85 Cryo-EM structure of human dynactin complex bound to Chlamydia effector Dre1 Deposited 2024-03-28 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 × 19 PDB declaration: 19-meric
Chain N 1–286（286 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9EC0 Structure of the CARMIL dimer bound to Capping Protein Deposited 2024-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–286（286 aa）
Chain E 1–286（286 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9Y9L CP at the barbed end with one cofilin on second-to-last subunit Deposited 2025-09-14 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 × 11 PDB declaration: 11-meric
Chain Y 1–286（286 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
9Y9M Capping protein bound to the barbed end of cofilactin Deposited 2025-09-14 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 × 10 PDB declaration: decameric
Chain Y 1–277（277 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
9YIM Capping protein bound to the barbed end of F-actin Deposited 2025-10-01 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 × 7 PDB declaration: heptameric
Chain Y 8–285（278 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAZA1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain X； PDBConstruct 1–12； UniProt 265–276 Author chain Y； PDBConstruct 1–12； UniProt 265–276

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 1mwn

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1mwn
Deposition date deposition_date2002-09-30
Structure title titleSolution NMR structure of S100B bound to the high-affinity target peptide TRTK-12
Keywords keywords;S100B, TRTK-12, Calcium-binding, EF-hand, S100 protein, four helix bundle, helix loop helix, protein-peptide complex, 20 structures, structural protein ;; STRUCTURAL PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.40 Å
Radius of gyration Rg (electron density) rg_electron17.79 Å
Forward intensity I(0) i03370370000.00
Molecular weight molecular_weight486190.0 kDa
Excluded volume excluded_volume603340 ų
Envelope volume envelope_volume60973 ų
Hydration-shell volume shell_volume24137 ų
Envelope diameter envelope_diameter69.0 Å
Shell Rg shell_rg27.83 Å
Envelope Rg envelope_rg20.90 Å
Shape Rg shape_rg17.81 Å
Total Rg total_rg17.84 Å
Total atoms total_atoms66600
Residues n_residues4120
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 dmax60.9 Å
Rg (real space) rg_real18.31 Å
Rg uncertainty (real space) rg_real_error0.48 Å
I(0) (real space) i0_real3.3700e+09
I(0) uncertainty (real space) i0_real_error4.8790e+07
Rg (reciprocal space) rg_reciprocal18.32 Å
I(0) (reciprocal space) i0_reciprocal3370000000.0000
Solution quality estimate total_estimate0.8017
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary21.7 Å
Skewness Skewness skewness0.157
Kurtosis Kurtosis kurtosis-0.443
Angular range angular_range— – 0.4300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1248000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.807; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1mwna_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd1mwnb_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins

CATH v4.4 (2 domains)

Domain ID domain_id1mwnA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1mwnB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
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8. Citations (4)

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9. Files and Curves (10)