[English] 日本語
Yorodumi
- PDB-3ryh: GMPCPP-Tubulin: RB3 Stathmin-like domain complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ryh
TitleGMPCPP-Tubulin: RB3 Stathmin-like domain complex
Components
  • Stathmin-4
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / GMPCPP / GTPASE / MICROTUBULE / STATHMIN S-TUBULIN / SUBTILISIN / TUBULIN
Function / homology
Function and homology information


axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior ...axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior / microtubule depolymerization / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / locomotory exploration behavior / startle response / microtubule polymerization / regulation of microtubule polymerization or depolymerization / response to tumor necrosis factor / microtubule-based process / response to mechanical stimulus / homeostasis of number of cells within a tissue / condensed chromosome / cellular response to calcium ion / tubulin binding / adult locomotory behavior / synapse organization / intracellular protein transport / neuron migration / neuromuscular junction / visual learning / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / cerebral cortex development / memory / recycling endosome / neuron projection development / gene expression / growth cone / neuron apoptotic process / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin alpha chain / Stathmin-4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
OVIS ARIES (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNawrotek, A. / Knossow, M. / Gigant, B.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Determinants That Govern Microtubule Assembly from the Atomic Structure of GTP-Tubulin.
Authors: Nawrotek, A. / Knossow, M. / Gigant, B.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Tubulin alpha chain
B: Tubulin beta chain
C: Tubulin alpha chain
D: Tubulin beta chain
E: Stathmin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,19721
Polymers217,2435
Non-polymers2,95416
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21560 Å2
ΔGint-227 kcal/mol
Surface area66920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.270, 128.210, 250.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) OVIS ARIES (sheep) / Organ: Brain / References: UniProt: D0VWZ0
#2: Protein Tubulin beta chain


Mass: 50043.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) OVIS ARIES (sheep) / Organ: Brain / References: UniProt: D0VWY9
#3: Protein Stathmin-4 / / RB3-SLD / Stathmin-like protein B3 / RB3


Mass: 16745.975 Da / Num. of mol.: 1 / Fragment: Residues 48-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: STMN4 / Plasmid: PET-8C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63043

-
Non-polymers , 5 types, 208 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-CPP, energy-carrying molecule analogue*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsAUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN SEQUENCE WAS ...AUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN SEQUENCE WAS USED FOR REFINEMENT BECAUSE THE SEQUENCE OF OVINE BRAIN TUBULIN IS NOT AVAILABLE. FOR BETA-TUBULIN (CHAIN B AND CHAIN D), THERE ARE THREE MAJOR ISOTYPES EXPRESSED IN THE BRAIN. THEY MAINLY USED THE BETA 2B ISOTYPE SEQUENCE (NCBI NP_001003900.1), BUT INTRODUCED POINT MUTATIONS WHEN POSSIBLE TO TAKE INTO ACCOUNT THE ISOTYPE DIVERSITY. SPECIFICALLY, RESIDUE THR 33 IS FOUND IN 75% OF TUBULIN MOLECULES (25% IS SER). IT IS REFINED WITH THR BUT WITH AN 75% OCCUPANCY FOR THE CG2 ATOM. RESIDUE 172: MET (60%) OR VAL (40%), REFINED WITH MET, BUT WITH OCCUPANCY 0.6 FOR SD AND CE ATOMS. RESIDUE 220: A MIX OF THR (75%) AND ALA (25%), REFINED WITH THR, OCCUPANCY 0.75 FOR OG1 AND CG2 ATOMS. AT POSITION 277, A MIX OF SER (75%) AND ALA (25%), REFINED WITH SER BUT WITH OCCUPANCY O.75 FOR OG ATOM. RESIDUE 298: SAME AS ABOVE BUT WITH SER 60% AND ALA 40%, REFINED WITH SER BUT WITH OCCUPANCY O.60 FOR OG ATOM. POSITION 317: THR 25%, ALA 75%, REFINED WITH A THR BUT WITH AN 0.25 OCCUPANCY FOR THE OG1 AND CG2 ATOMS. RESIDUE 318: ILE (60%) OR VAL (40%), REFINED WITH ILE, WITH OCCUPANCY 0.6 FOR CD1 ATOM. RESIDUE 335: THE SAME AS ABOVE BUT WITH ILE 25% AND VAL 75%, REFINED WITH ILE, WITH OCCUPANCY 0.25 FOR CD1 ATOM. RESIDUE 375, A MIX OF ALA (0.75) AND SER (0.25) AT THIS POSITION, REFINED WITH SER, OCCUPANCY 0.25 FOR OG ATOM. THE STATHMIN-4 FRAGMENT (CHAIN E) USED IN THIS STUDY INCLUDES A N-TERMINAL ALA RESIDUE, WHICH IS ACETYLATED, AND HAS TWO POINT MUTATIONS (CYS14 TO ALA AND PHE20 TO TRP, STATHMIN NUMBERING).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG, LISO4, PIPES BUFFER, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→45 Å / Num. obs: 51713 / % possible obs: 99.3 % / Redundancy: 4 % / Biso Wilson estimate: 71.66 Å2 / Rsym value: 0.101 / Net I/σ(I): 10.2
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2 / Rsym value: 0.66 / % possible all: 89

-
Processing

Software
NameVersionClassification
AMoREphasing
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HKB

3hkb


Resolution: 2.8→42.13 Å / Cor.coef. Fo:Fc: 0.9515 / Cor.coef. Fo:Fc free: 0.9217 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 2583 5 %RANDOM
Rwork0.165 ---
obs0.1676 51617 --
Displacement parametersBiso mean: 84.4 Å2
Baniso -1Baniso -2Baniso -3
1--22.4441 Å20 Å20 Å2
2--11.8103 Å20 Å2
3---10.6338 Å2
Refine analyzeLuzzati coordinate error obs: 0.401 Å
Refinement stepCycle: LAST / Resolution: 2.8→42.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14623 0 172 192 14987
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115248HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1920701HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5272SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes425HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2201HARMONIC5
X-RAY DIFFRACTIONt_it15248HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion20.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1988SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17723SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3141 177 5.01 %
Rwork0.2307 3355 -
all0.2347 3532 -
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)
11.2487-0.882-0.41192.19350.51461.53220.0530.2374-0.1881-0.0839-0.20670.01380.32650.09010.15370.75810.06140.02590.0722-0.0827-0.05338.842832.358574.3165
21.2499-1.2396-0.29893.70930.7481.12940.13520.12340.1786-0.3057-0.1196-0.4788-0.07050.1378-0.01560.42870.00570.075-0.11190.0016-0.1483-0.201271.056690.5696
31.0735-1.2595-0.35523.24680.81911.2987-0.04580.01230.1477-0.1888-0.0403-0.434-0.20320.09680.08610.57770.0197-0.0373-0.0638-0.0613-0.0078-14.7862109.47102.387
42.1484-1.5697-0.88392.70810.90192.42050.38270.28790.0618-0.4594-0.3642-0.1044-0.39460.0171-0.01850.65810.0875-0.01750.06-0.0624-0.0133-35.8691143.086115.515
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|614 E|4 - E|64 }A1 - 614
2X-RAY DIFFRACTION1{ A|1 - A|614 E|4 - E|64 }E4 - 64
3X-RAY DIFFRACTION2{ B|1 - B|612 E|65 - E|89 }B1 - 612
4X-RAY DIFFRACTION2{ B|1 - B|612 E|65 - E|89 }E65 - 89
5X-RAY DIFFRACTION3{ C|1 - C|614 E|90 - E|115 }C1 - 614
6X-RAY DIFFRACTION3{ C|1 - C|614 E|90 - E|115 }E90 - 115
7X-RAY DIFFRACTION4{ D|1 - D|615 E|116 - E|145 }D1 - 615
8X-RAY DIFFRACTION4{ D|1 - D|615 E|116 - E|145 }E116 - 145

+
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