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- PDB-7e1t: Crystal structure of Rab9A-GTP-Nde1 -

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Basic information

Entry
Database: PDB / ID: 7e1t
TitleCrystal structure of Rab9A-GTP-Nde1
Components
  • Isoform 2 of Nuclear distribution protein nudE homolog 1
  • Ras-related protein Rab-9A
KeywordsPROTEIN TRANSPORT / Rab9A / Nde1 / Rab GTPase / effector
Function / homology
Function and homology information


negative regulation by host of symbiont catalytic activity / : / ciliary basal body-plasma membrane docking / kinetochore => GO:0000776 / establishment of chromosome localization / Rab protein signal transduction / Retrograde transport at the Trans-Golgi-Network / vesicle transport along microtubule / RAB geranylgeranylation / RHOBTB3 ATPase cycle ...negative regulation by host of symbiont catalytic activity / : / ciliary basal body-plasma membrane docking / kinetochore => GO:0000776 / establishment of chromosome localization / Rab protein signal transduction / Retrograde transport at the Trans-Golgi-Network / vesicle transport along microtubule / RAB geranylgeranylation / RHOBTB3 ATPase cycle / microtubule nucleation / RAB GEFs exchange GTP for GDP on RABs / spindle pole centrosome / retrograde transport, endosome to Golgi / mitotic centrosome separation / centrosome localization / kinesin complex / positive regulation of exocytosis / establishment of mitotic spindle orientation / cleavage furrow / centrosome duplication / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / phagocytic vesicle / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / transport vesicle / 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 / regulation of G2/M transition of mitotic cell cycle / AURKA Activation by TPX2 / mitotic spindle organization / trans-Golgi network membrane / chromosome segregation / RHO GTPases Activate Formins / cerebral cortex development / kinetochore / phagocytic vesicle membrane / GDP binding / Separation of Sister Chromatids / regulation of protein localization / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / melanosome / cell migration / protein transport / late endosome / microtubule binding / microtubule / cell differentiation / lysosome / cell division / Golgi membrane / GTPase activity / centrosome / GTP binding / endoplasmic reticulum membrane / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
NUDE domain / NUDE family / NUDE protein, C-terminal conserved region / Rab9 / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family ...NUDE domain / NUDE family / NUDE protein, C-terminal conserved region / Rab9 / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-9A / Nuclear distribution protein nudE homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsZhang, Y. / Zhang, T. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31530013 and 31870722 China
CitationJournal: Structure / Year: 2022
Title: Nde1 is a Rab9 effector for loading late endosomes to cytoplasmic dynein motor complex.
Authors: Zhang, Y. / Chen, Z. / Wang, F. / Sun, H. / Zhu, X. / Ding, J. / Zhang, T.
History
DepositionFeb 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-9A
B: Ras-related protein Rab-9A
C: Isoform 2 of Nuclear distribution protein nudE homolog 1
D: Isoform 2 of Nuclear distribution protein nudE homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1518
Polymers63,0564
Non-polymers1,0954
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-55 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.421, 67.646, 118.516
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ras-related protein Rab-9A


Mass: 22977.727 Da / Num. of mol.: 2 / Fragment: GTPase domain / Mutation: Q66L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB9A, RAB9 / Plasmid: pETM30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P51151
#2: Protein Isoform 2 of Nuclear distribution protein nudE homolog 1 / NudE


Mass: 8550.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDE1, NUDE / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NXR1
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 5.5 / Details: 0.1 M Bis-Tris, pH 5.5 and 25% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 7, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.45→47.75 Å / Num. obs: 18238 / % possible obs: 88.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 30.3 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.5
Reflection shellResolution: 2.45→2.51 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 912 / CC1/2: 0.715 / % possible all: 65.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QXA

4qxa


Resolution: 2.45→47.75 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / SU B: 19.188 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 926 5.1 %RANDOM
Rwork0.1937 ---
obs0.1962 17293 88.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.69 Å2 / Biso mean: 37.781 Å2 / Biso min: 14.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å2-0 Å2
2---1.18 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 2.45→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 66 153 3439
Biso mean--34.59 40.94 -
Num. residues----402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023359
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9674554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93424.368174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87515563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9651523
X-RAY DIFFRACTIONr_chiral_restr0.0580.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022555
X-RAY DIFFRACTIONr_rigid_bond_restr16.97133266
X-RAY DIFFRACTIONr_sphericity_bonded24.25753203
LS refinement shellResolution: 2.45→2.514 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 51 -
Rwork0.279 944 -
all-995 -
obs--65.76 %
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)
10.0274-0.02880.03890.0707-0.10450.15870.0047-0.01340.0038-0.00170.0018-0.00280.0007-0.0096-0.00650.0016-0.0010.00250.0952-0.0030.03482.8189-19.5085-7.5905
20.31660.11240.04570.0859-0.00890.29870.01010.0087-0.0012-0.0070.009-0.01120.03340.0102-0.01910.01520.007-0.00160.0931-0.0030.015617.5434-50.163922.9387
30.0071-0.0152-0.03650.03370.07480.21570.00280.00660.0032-0.0067-0.0231-0.0128-0.0157-0.03730.02030.0023-0.00520.00280.1080.01130.05491.5847-41.76893.2712
40.1554-0.16810.04510.182-0.04880.0131-0.0324-0.0210.0180.03780.0248-0.0171-0.0101-0.00590.00760.0102-0.0121-0.00450.12290.00190.03725.1228-33.073311.477
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 175
2X-RAY DIFFRACTION2B6 - 179
3X-RAY DIFFRACTION3C98 - 130
4X-RAY DIFFRACTION4D97 - 121

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