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4dzo

Structure of Human Mad1 C-terminal Domain Reveals Its Involvement in Kinetochore Targeting

Method: X-RAY DIFFRACTION Dmax: 83.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Mitotic spindle assembly checkpoint protein MAD1

Homo sapiens

UniProt Q9Y6D9

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 597–718 Chain B； UniProt 597–718 Fragment：C-terminal domain, UNP residues 597-718 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：hanging-drop vapor diffusion；pH 6.2；293 K；20 mM Tris, 100 mM KCl, 1 mM TCEP, 26% (w/v) PEG1500, 0.1 M Na Cacodylate, pH 6.2, 1mM reduced L-Glutathione;, hanging-drop vapor diffusion, temperature 293K Resolution 1.76 Å R-free 0.197

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 4DZO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GO4 Crystal structure of Mad1-Mad2 reveals a conserved Mad2 binding motif in Mad1 and Cdc20. Deposited 2001-10-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 393–492（100 aa） Fragment：RESIDUES 485-584
Chain F 393–492（100 aa） Fragment：RESIDUES 485-584
Chain G 393–492（100 aa） Fragment：RESIDUES 485-584
Chain H 393–492（100 aa） Fragment：RESIDUES 485-584
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；PROTEIN CONCENTRATION 7.5 MG/ML HANGING DROP METHOD, WELL=100 MM AMMONIUM SULPHATE, 100 MM AMMONIUM CITRATE PH 5.2, 10 MM DTT
Resolution 2.05 Å R-free 0.268
7B1F Orthorhombic P212121 Structure of Human Mad1 C-terminal Domain in Complex with Phosphorylated Bub1 CD1 Domain Deposited 2020-11-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 597–718（122 aa）
Chain B 597–718（122 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 4000, 0.1 M Hepes pH 7.5, 10% isopropanol
Resolution 1.75 Å R-free 0.287
7B1H Monoclinic P21 Structure of Human Mad1 C-terminal Domain in Complex with Phosphorylated Bub1 CD1 Domain Deposited 2020-11-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 597–718（122 aa）
Chain B 597–718（122 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；8% Isopropanol, 20% PEG 4000, 0.1 M Na HEPES, pH 7.5
Resolution 2.40 Å R-free 0.281
7B1H Monoclinic P21 Structure of Human Mad1 C-terminal Domain in Complex with Phosphorylated Bub1 CD1 Domain Deposited 2020-11-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 597–718（122 aa）
Chain F 597–718（122 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；8% Isopropanol, 20% PEG 4000, 0.1 M Na HEPES, pH 7.5
Resolution 2.40 Å R-free 0.281
7B1J Orthorhombic P21212 Structure of Human Mad1 C-terminal Domain in Complex with Phosphorylated Bub1 CD1 Domain Deposited 2020-11-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 597–718（122 aa）
Chain B 597–718（122 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；10% Isopropanol, 0.1 M Na HEPES, pH 7.5, 20% PEG 4000
Resolution 2.90 Å R-free 0.296

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

View Construct and Data Evidence
UniProt name MD1L1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–123； UniProt 597–718 Author chain B； PDBConstruct 2–123； UniProt 597–718

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 4dzo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4dzo
Deposition date deposition_date2012-03-01
Structure title titleStructure of Human Mad1 C-terminal Domain Reveals Its Involvement in Kinetochore Targeting
Keywords keywordshomodimer, kinetochore, mitosis, spindle checkpoint protein, Mad2, nucleus, CELL CYCLE; CELL CYCLE
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_guinier23.02 Å
Radius of gyration Rg (electron density) rg_electron22.75 Å
Forward intensity I(0) i013045700.00
Molecular weight molecular_weight27292.0 kDa
Excluded volume excluded_volume34240 ų
Envelope volume envelope_volume42727 ų
Hydration-shell volume shell_volume17567 ų
Envelope diameter envelope_diameter84.0 Å
Shell Rg shell_rg26.39 Å
Envelope Rg envelope_rg23.96 Å
Shape Rg shape_rg22.73 Å
Total Rg total_rg23.34 Å
Total atoms total_atoms3849
Residues n_residues235
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 dmax83.8 Å
Rg (real space) rg_real23.36 Å
Rg uncertainty (real space) rg_real_error0.82 Å
I(0) (real space) i0_real1.3050e+07
I(0) uncertainty (real space) i0_real_error2.0240e+05
Rg (reciprocal space) rg_reciprocal23.28 Å
I(0) (reciprocal space) i0_reciprocal13050000.0000
Solution quality estimate total_estimate0.7747
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.9 Å
Skewness Skewness skewness0.747
Kurtosis Kurtosis kurtosis0.160
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2184000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.497; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.628; Smooth: 0.947
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4dzoA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily170 —
Domain ID domain_id4dzoA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology457 — Copper Amine Oxidase; Chain A, domain 1
Homologous superfamily homologous superfamily60 —
Domain ID domain_id4dzoB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily170 —
Domain ID domain_id4dzoB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology457 — Copper Amine Oxidase; Chain A, domain 1
Homologous superfamily homologous superfamily60 —
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8. Citations (4)

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9. Files and Curves (10)