[English] 日本語
Yorodumi
- PDB-4dzo: Structure of Human Mad1 C-terminal Domain Reveals Its Involvement... -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of metaphase plate congression / cytoplasmic sequestering of protein / kinetochore binding / nuclear pore nuclear basket / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle assembly checkpoint signaling ...MAD1 complex / deactivation of mitotic spindle assembly checkpoint / mitotic spindle assembly checkpoint MAD1-MAD2 complex / positive regulation of mitotic cell cycle spindle assembly checkpoint / regulation of metaphase plate congression / cytoplasmic sequestering of protein / kinetochore binding / nuclear pore nuclear basket / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle assembly checkpoint signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / negative regulation of T cell proliferation / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / thymus development / RHO GTPases Activate Formins / mitotic spindle / kinetochore / spindle pole / spindle / Separation of Sister Chromatids / nuclear envelope / cell division / centrosome / identical protein binding / nucleus / cytosol / cytoplasm
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more