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- PDB-4dzo: Structure of Human Mad1 C-terminal Domain Reveals Its Involvement... -

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Basic information

Entry
Database: PDB / ID: 4dzo
TitleStructure of Human Mad1 C-terminal Domain Reveals Its Involvement in Kinetochore Targeting
ComponentsMitotic spindle assembly checkpoint protein MAD1
KeywordsCELL CYCLE / homodimer / kinetochore / mitosis / spindle checkpoint protein / Mad2 / nucleus
Function / homology
Function and homology information


MAD1 complex / deactivation of mitotic spindle assembly checkpoint / mitotic spindle assembly checkpoint MAD1-MAD2 complex / positive regulation of mitotic cell cycle spindle assembly checkpoint / kinetochore binding / nuclear pore nuclear basket / regulation of metaphase plate congression / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle assembly checkpoint signaling / negative regulation of T cell proliferation ...MAD1 complex / deactivation of mitotic spindle assembly checkpoint / mitotic spindle assembly checkpoint MAD1-MAD2 complex / positive regulation of mitotic cell cycle spindle assembly checkpoint / kinetochore binding / nuclear pore nuclear basket / regulation of metaphase plate congression / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle assembly checkpoint signaling / negative regulation of T cell proliferation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / thymus development / RHO GTPases Activate Formins / kinetochore / spindle / spindle pole / mitotic spindle / Separation of Sister Chromatids / nuclear envelope / cell division / centrosome / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Copper Amine Oxidase; Chain A, domain 1 - #60 / Spindle assembly checkpoint component Mad1 / Mitotic checkpoint protein / Copper Amine Oxidase; Chain A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Mitotic spindle assembly checkpoint protein MAD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsLuo, X. / Sun, H. / Tomchick, D.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of human Mad1 C-terminal domain reveals its involvement in kinetochore targeting.
Authors: Kim, S. / Sun, H. / Tomchick, D.R. / Yu, H. / Luo, X.
#1: Journal: Structure / Year: 2008
Title: Protein metamorphosis: the two-state behavior of Mad2.
Authors: Luo, X. / Yu, H.
#2: Journal: Nat. Struct. Mol. Biol. / Year: 2004
Title: The Mad2 spindle checkpoint protein has two distinct natively folded states.
Authors: Luo, X. / Tang, Z. / Xia, G. / Wassmann, K. / Matsumoto, T. / Rizo, J. / Yu, H.
#3: Journal: Mol. Cell / Year: 2002
Title: The Mad2 spindle checkpoint protein undergoes similar major conformational changes upon binding to either Mad1 or Cdc20.
Authors: Luo, X. / Tang, Z. / Rizo, J. / Yu, H.
History
DepositionMar 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_monochromatic_or_laue_m_l
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitotic spindle assembly checkpoint protein MAD1
B: Mitotic spindle assembly checkpoint protein MAD1


Theoretical massNumber of molelcules
Total (without water)28,1322
Polymers28,1322
Non-polymers00
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-45 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.767, 44.767, 211.056
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Mitotic spindle assembly checkpoint protein MAD1 / Mitotic arrest deficient 1-like protein 1 / MAD1-like protein 1 / Mitotic checkpoint MAD1 protein ...Mitotic arrest deficient 1-like protein 1 / MAD1-like protein 1 / Mitotic checkpoint MAD1 protein homolog / HsMAD1 / hMAD1 / Tax-binding protein 181


Mass: 14065.779 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 597-718
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAD1, MAD1L1, TXBP181 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y6D9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: hanging-drop vapor diffusion / pH: 6.2
Details: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2008 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.76→33.96 Å / Num. all: 23608 / Num. obs: 23608 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Biso Wilson estimate: 19.83 Å2 / Limit h max: 21 / Limit h min: 0 / Limit k max: 22 / Limit k min: 0 / Limit l max: 119 / Limit l min: 0 / Rmerge(I) obs: 0.081 / Χ2: 1.751 / Net I/σ(I): 10.2
Reflection scaleGroup code: 1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.76-1.7911.50.67612021.181198.6
1.79-1.8214.30.56411471.0951100
1.82-1.8614.90.4512081.0871100
1.86-1.9150.40711471.1111100
1.9-1.94150.29712041.0871100
1.94-1.98150.25611561.151100
1.98-2.0315.10.19512131.1321100
2.03-2.0915.10.16511471.1231100
2.09-2.15150.1411951.1661100
2.15-2.2215.10.11911811.191100
2.22-2.315.10.11311671.281100
2.3-2.3915.10.09811851.3031100
2.39-2.515.10.09112111.3771100
2.5-2.6315.10.07911771.5341100
2.63-2.7915.20.07111821.6741100
2.79-3.0115.10.06611692.0521100
3.01-3.3115.10.06511842.7071100
3.31-3.7914.80.06311933.4471100
3.79-4.7814.60.04911873.1111100
4.78-5014.70.05512255.054199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→33.955 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8957 / SU ML: 0.4 / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Phase error: 17.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 2034 8.62 %RANDOM
Rwork0.1604 ---
all0.1635 23583 --
obs0.1635 23583 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.01 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso max: 90.06 Å2 / Biso mean: 29.0947 Å2 / Biso min: 8.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.9251 Å2-0 Å2-0 Å2
2--0.9251 Å20 Å2
3----1.8501 Å2
Refine analyzeLuzzati sigma a obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 1.76→33.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 0 287 2201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111940
X-RAY DIFFRACTIONf_angle_d1.2052606
X-RAY DIFFRACTIONf_chiral_restr0.07303
X-RAY DIFFRACTIONf_plane_restr0.006329
X-RAY DIFFRACTIONf_dihedral_angle_d14.283736
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.76-1.8010.2681360.2341423155999
1.801-1.8460.24481400.212714481588100
1.846-1.89590.27231430.189714031546100
1.8959-1.95170.19781380.15914491587100
1.9517-2.01470.21251310.152714351566100
2.0147-2.08670.20271340.160114241558100
2.0867-2.17020.20641380.149714171555100
2.1702-2.2690.19791340.146414691603100
2.269-2.38860.19891330.143414271560100
2.3886-2.53820.21171340.151214441578100
2.5382-2.73410.19371330.152814371570100
2.7341-3.00910.17871330.156214421575100
3.0091-3.44410.21551380.160414551593100
3.4441-4.33780.1631340.153114231557100
4.3378-33.96120.18251350.171214531588100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.14360.3919-1.91540.5956-0.79956.5022-0.0368-0.30870.03740.04320.00210.04970.17240.27310.05160.08110.03170.00340.17510.01370.13537.713.3553130.4861
21.9482-0.00760.00112.57930.42422.02190.05060.09240.23090.0305-0.03350.1904-0.0142-0.1167-0.01670.08110.00820.02340.09250.03360.10626.768326.813298.5208
30.48170.523-1.79180.5856-1.10746.97340.0733-0.07870.11360.04950.03480.04790.0665-0.00120.01630.08030.01710.00110.1607-0.00740.1415-2.290414.6938129.3432
42.4061-0.41031.13261.2218-0.27272.11240.4433-0.2936-0.78490.25950.0738-0.25830.76840.089-0.17510.3319-0.0149-0.15010.13020.09910.31539.03474.9025105.1973
51.49290.03750.49791.23220.47630.99260.35710.5906-0.81-0.09590.0429-0.29320.25410.4029-0.24010.17660.072-0.02350.1627-0.06460.240211.39098.152692.8759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 598:637)A598 - 637
2X-RAY DIFFRACTION2chain 'A' and (resseq 638:716)A638 - 716
3X-RAY DIFFRACTION3chain 'B' and (resseq 596:637)B596 - 637
4X-RAY DIFFRACTION4chain 'B' and (resseq 638:682)B638 - 682
5X-RAY DIFFRACTION5chain 'B' and (resseq 683:718)B683 - 718

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