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- PDB-3ryh: GMPCPP-Tubulin: RB3 Stathmin-like domain complex -

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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 / startle response / locomotory exploration behavior / microtubule polymerization / regulation of microtubule polymerization or depolymerization / response to tumor necrosis factor / condensed chromosome / response to mechanical stimulus / homeostasis of number of cells within a tissue / cellular response to calcium ion / tubulin binding / adult locomotory behavior / intracellular protein transport / neuron migration / synapse organization / visual learning / neuromuscular junction / recycling endosome / cerebral cortex development / structural constituent of cytoskeleton / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / mitotic cell cycle / 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; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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Non-polymers , 5 types, 208 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-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


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


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

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Details

Has protein modificationN
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).

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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: 2.41 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

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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

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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

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