[English] 日本語
Yorodumi
- PDB-2r8u: Structure of fragment of human end-binding protein 1 (EB1) contai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r8u
TitleStructure of fragment of human end-binding protein 1 (EB1) containing the N-terminal domain at 1.35 A resolution
ComponentsMicrotubule-associated protein RP/EB family member 1
KeywordsCELL CYCLE / cytoskeleton / Acetylation / Cell division / Cytoplasm / Microtubule / Mitosis / Phosphorylation
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
MOLYBDATE ION / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.35 Å
AuthorsHuang, X. / Lovelace, L.L. / Smith, D. / Lebioda, L.
CitationJournal: To be Published
Title: Structure of fragment of human end-binding protein 1 (EB1) containing the N-terminal domain at 1.35 A resolution
Authors: Huang, X. / Lovelace, L.L. / Smith, D. / Lebioda, L.
History
DepositionSep 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2243
Polymers60,0642
Non-polymers1601
Water4,684260
1
A: Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1922
Polymers30,0321
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)30,0321
Polymers30,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.890, 47.921, 100.663
Angle α, β, γ (deg.)90.000, 91.650, 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 / End-binding protein 1 / EB1


Mass: 30032.020 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15691
#2: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tris, 0.1M Na2MoO4, 35% PEG4000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 66996 / Num. obs: 50648 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 17.9
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.284

-
Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
CNSphasing
SHELXL-97refinement
RefinementMethod to determine structure: AB INITIO
Starting model: pdb entry 1pa7

1pa7


Resolution: 1.35→10 Å / Num. parameters: 21846 / Num. restraintsaints: 26490 / Cross valid method: FREE R / σ(F): 0 / σ(I): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2114 -RANDOM
Rwork0.164 ---
all0.176 66996 --
obs0.176 50641 76 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 29.28 Å2
Refinement stepCycle: LAST / Resolution: 1.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 5 260 2427
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.023
X-RAY DIFFRACTIONs_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.047
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.057
X-RAY DIFFRACTIONs_approx_iso_adps0.076
LS refinement shellResolution: 1.35→1.39 Å /
Num. reflection% reflection
obs50648 75.6 %

+
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