[English] 日本語
Yorodumi
- PDB-1vka: Southeast Collaboratory for Structural Genomics: Hypothetical Hum... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vka
TitleSoutheast Collaboratory for Structural Genomics: Hypothetical Human Protein Q15691 N-Terminal Fragment
ComponentsMicrotubule-associated protein RP/EB family member 1
KeywordsStructural Genomics / unknown function / Q15691 / Homo sapiens / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation ...protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / protein localization to centrosome / microtubule organizing center / negative regulation of microtubule polymerization / mitotic spindle pole / microtubule polymerization / establishment of mitotic spindle orientation / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / protein localization / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / cell migration / microtubule / molecular adaptor activity / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / RNA binding / identical protein binding / cytosol
Similarity search - Function
EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily ...EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / sulfur sas / SAD / Resolution: 1.6 Å
AuthorsLiu, Z.-J. / Tempel, W. / Schubot, F.D. / Shah, A. / Dailey, T.A. / Mayer, M.R. / Rose, J.P. / Dailey, H.A. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: TO BE PUBLISHED
Title: Southeast Collaboratory for Structural Genomics: Hypothetical Human Protein Q15691 N-Terminal Fragment
Authors: Liu, Z.-J. / Tempel, W. / SCHUBOT, F.D. / SHAH, A. / ROSE, J.P. / RICHARDSON, D.C. / RICHARDSON, J.S. / Wang, B.-C.
History
DepositionMay 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE THE STRUCTURE PRESENTED IN THIS ENTRY IS A PROTOLYTIC FRAGMENT (RESIDUES (2-140) OF THE ...SEQUENCE THE STRUCTURE PRESENTED IN THIS ENTRY IS A PROTOLYTIC FRAGMENT (RESIDUES (2-140) OF THE MATURE Q15691 PROTEIN.
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Microtubule-associated protein RP/EB family member 1
B: Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)34,7922
Polymers34,7922
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.951, 47.582, 100.690
Angle α, β, γ (deg.)90.000, 91.741, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1


Mass: 17395.861 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: The protein was cloned, expressed and purified by the SECSG human protein production group (T.A. Dailey, M. Mayer) under the direction H.A. Dailey.
Gene: MAPRE1 / Cell line (production host): BL21(DE53) / Production host: Escherichia coli (E. coli) / Keywords: APC-binding protein, Q15691, sulfur SAS / References: UniProt: Q15691
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: clear colorless prism
Crystal growTemperature: 291 K / Method: micro-batch under oil / pH: 6.2 / Details: pH 6.2, Micro-batch under oil, temperature 291K

-
Data collection

Diffraction
IDCrystal-ID
q156911
11
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2003
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 37287 / % possible obs: 98.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.2
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obs
1.6-1.6696.70.107
3.45-5093.70.033
2.74-3.4599.50.036
2.39-2.7499.60.039
2.17-2.3999.30.041
2.02-2.1799.10.045
1.9-2.0298.80.052
1.8-1.998.60.062
1.72-1.898.30.073
1.66-1.7298.20.087

-
Phasing

PhasingMethod: SAD
Phasing MADD res high: 3 Å / D res low: 20 Å / FOM : 0.38 / Reflection: 4962
Phasing MAD shell
Resolution (Å)FOM Reflection
9.91-200.34158
6.56-9.910.41446
5.22-6.560.39545
4.46-5.220.38631
3.96-4.460.38703
3.6-3.960.39777
3.32-3.60.36822
3.09-3.320.35880
Phasing dmFOM : 0.59 / FOM acentric: 0.63 / FOM centric: 0.4 / Reflection: 5492 / Reflection acentric: 4544 / Reflection centric: 948
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.3-9.9730.780.780.51147539
5.2-8.30.630.720.38780586194
4.1-5.20.690.750.46960772188
3.6-4.10.70.730.57946787159
3.1-3.60.580.620.3516741439235
2.9-3.10.350.360.221018885133

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefmac_5.1.24refinement
HKL-2000data reduction
ARP/wARPmodel building
RefinementMethod to determine structure: sulfur sas / Resolution: 1.6→100 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.367 / SU ML: 0.05 / SU R Cruickshank DPI: 0.093 / ESU R Free: 0.086
Details: THE Q15691 STRUCTURE WAS INITIALLY SOLVED TO 3 ANGSTROMS IN SPACE GROUP P 21 21 21 USING A SET OF SULFUR SAS DATA COLLECTED WITH FOCUSED CHROMIUM X-RAYS (LAMBDA = 2.29 ANGSTROMS). THE MODEL ...Details: THE Q15691 STRUCTURE WAS INITIALLY SOLVED TO 3 ANGSTROMS IN SPACE GROUP P 21 21 21 USING A SET OF SULFUR SAS DATA COLLECTED WITH FOCUSED CHROMIUM X-RAYS (LAMBDA = 2.29 ANGSTROMS). THE MODEL PRESENTED IN THIS ENTRY WAS REFINED AGAINST 1.6 ANGSTROM DATA COLLECTED AT SER-CAT (22ID) ON A BETTER DIFFRACTING MONOCLINIC CRYSTAL.
RfactorNum. reflection% reflection
Rfree0.2137 1964 5.004 %
Rwork0.1998 --
all0.201 --
obs-37287 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 15.686 Å2
Baniso -1Baniso -2Baniso -3
1--0.551 Å20 Å2-0.078 Å2
2--0.595 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 0 201 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222120
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9312866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8715262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.0860.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021615
X-RAY DIFFRACTIONr_nbd_refined0.1930.2953
X-RAY DIFFRACTIONr_nbtor_refined0.310.21535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2125
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.25
X-RAY DIFFRACTIONr_mcbond_it0.741.51303
X-RAY DIFFRACTIONr_mcangle_it1.3622086
X-RAY DIFFRACTIONr_scbond_it2.1353817
X-RAY DIFFRACTIONr_scangle_it3.3374.5780
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.599-1.64080.2391360.19525292927
1.641-1.68580.2221460.18627152926
1.686-1.73460.2021460.18625682754
1.735-1.7880.2311120.225562721
1.788-1.84660.2311440.19724482628
1.847-1.91140.2231300.19623932556
1.911-1.98350.2481200.19923422496
1.984-2.06450.231110.19921862316
2.064-2.15620.2151060.20221592287
2.156-2.26140.1981050.20320692192
2.261-2.38370.1761040.19619522068
2.384-2.52820.193890.19918581956
2.528-2.70260.2131020.20617441852
2.703-2.9190.215870.21216261720
2.919-3.19730.205960.20115101613
3.197-3.57420.24740.20413401436
3.574-4.12630.204600.18611701266
4.126-5.05150.186430.18310081089
5.052-7.13480.228390.217775852
7.135-1000.262140.266339486

+
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