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6kdr

Crystal structure of human NRMT2 in complex with human centromere protein B peptide

Method: X-RAY DIFFRACTION Dmax: 89.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha N-terminal protein methyltransferase 1B

Homo sapiens

UniProt Q5VVY1

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 61–283 Chain B； UniProt 61–283 Fragment：Protein N-terminal methyltransferase Peptide from Major centromere autoantigen B × 2 （P07199） SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 GOL GLYCEROL × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8.3；291 K；0.1M Tris pH 8.3, 6% w/v Polyethylene glycol 8000 Resolution 2.11 Å R-free 0.205

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 6KDR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5UBB Crystal structure of human alpha N-terminal protein methyltransferase 1B Deposited 2016-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 58–278（221 aa） Fragment：UNP residues 58-278
Not recorded SAM S-ADENOSYLMETHIONINE × 2 UNX UNKNOWN LIGAND × 52 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M sodium acetate
Resolution 2.00 Å R-free 0.250
6DUB Crystal structure of a methyltransferase Deposited 2018-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 58–278（221 aa） Fragment：UNP residues 58-278
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 2 UNX UNKNOWN LIGAND × 37 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000, 0.1 M potassium thiocyanate
Resolution 1.20 Å R-free 0.178
6DUB Crystal structure of a methyltransferase Deposited 2018-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 58–278（221 aa） Fragment：UNP residues 58-278
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 23 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000, 0.1 M potassium thiocyanate
Resolution 1.20 Å R-free 0.178
6KDS Crystal structure of human NRMT2 in complex with alpha-N-monomethylated human CENP-A peptide Deposited 2019-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 61–283（223 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.1；291 K；0.1M Tris pH 8.1, 14% w/v Polyethylene glycol 8000
Resolution 1.84 Å R-free 0.205

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NTM1B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 22–244； UniProt 61–283 Author chain B； PDBConstruct 22–244； UniProt 61–283

Peptide from Major centromere autoantigen B

OrganismNot specified

UniProt P07199

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 2–10 Chain E； UniProt 2–10 Not recorded Alpha N-terminal protein methyltransferase 1B × 2 （Q5VVY1） SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 GOL GLYCEROL × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8.3；291 K；0.1M Tris pH 8.3, 6% w/v Polyethylene glycol 8000 Resolution 2.11 Å R-free 0.205

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 6KDR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BW6 HUMAN CENTROMERE PROTEIN B (CENP-B) DNA BINDIGN DOMAIN RP1 Deposited 1998-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–56（56 aa） Fragment：DNA-BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 400 mM NA2SO4
Resolution not provided
1HLV CRYSTAL STRUCTURE OF CENP-B(1-129) COMPLEXED WITH THE CENP-B BOX DNA Deposited 2000-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–129（129 aa） Fragment：DNA BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；MPD, potassium cacodylate, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.260
1UFI Crystal structure of the dimerization domain of human CENP-B Deposited 2003-05-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 540–599（60 aa） Fragment：dimerization domain
Chain B 540–599（60 aa） Fragment：dimerization domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.7；293 K；sodium citrate, CHES, pH 9.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.65 Å R-free 0.309
1UFI Crystal structure of the dimerization domain of human CENP-B Deposited 2003-05-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 540–599（60 aa） Fragment：dimerization domain
Chain D 540–599（60 aa） Fragment：dimerization domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.7；293 K；sodium citrate, CHES, pH 9.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.65 Å R-free 0.309
1UFI Crystal structure of the dimerization domain of human CENP-B Deposited 2003-05-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 540–599（60 aa） Fragment：dimerization domain
Chain B 540–599（60 aa） Fragment：dimerization domain
Chain C 540–599（60 aa） Fragment：dimerization domain
Chain D 540–599（60 aa） Fragment：dimerization domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.7；293 K；sodium citrate, CHES, pH 9.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.65 Å R-free 0.309

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CENPB_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–9； UniProt 2–10 Author chain E； PDBConstruct 1–9； UniProt 2–10

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 6kdr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6kdr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6kdr
Deposition date deposition_date2019-07-02
Structure title titleCrystal structure of human NRMT2 in complex with human centromere protein B peptide
Keywords keywordscore methyltransferase fold, TRANSFERASE; TRANSFERASE
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_guinier26.81 Å
Radius of gyration Rg (electron density) rg_electron26.34 Å
Forward intensity I(0) i046322800.00
Molecular weight molecular_weight52668.0 kDa
Excluded volume excluded_volume65848 ų
Envelope volume envelope_volume77691 ų
Hydration-shell volume shell_volume25859 ų
Envelope diameter envelope_diameter91.4 Å
Shell Rg shell_rg32.30 Å
Envelope Rg envelope_rg26.33 Å
Shape Rg shape_rg26.37 Å
Total Rg total_rg26.88 Å
Total atoms total_atoms3689
Residues n_residues455
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 dmax89.0 Å
Rg (real space) rg_real27.01 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real4.6320e+07
I(0) uncertainty (real space) i0_real_error6.2190e+05
Rg (reciprocal space) rg_reciprocal26.95 Å
I(0) (reciprocal space) i0_reciprocal46320000.0000
Solution quality estimate total_estimate0.8328
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.7 Å
Skewness Skewness skewness0.500
Kurtosis Kurtosis kurtosis-0.449
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27880000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.722; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.786; Smooth: 0.870
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6kdrA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id6kdrB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
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8. Citations (1)

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9. Files and Curves (10)