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- PDB-4qxa: Crystal structure of the Rab9A-RUTBC2 RBD complex -

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Basic information

Entry
Database: PDB / ID: 4qxa
TitleCrystal structure of the Rab9A-RUTBC2 RBD complex
Components
  • Ras-related protein Rab-9A
  • Small G protein signaling modulator 1
KeywordsPROTEIN TRANSPORT/PROTEIN BINDING / PH domain / Rab9A / RUTBC2 / Rab binding domain / Rab9-effector complex / PROTEIN TRANSPORT-PROTEIN BINDING complex
Function / homology
Function and homology information


RHOBTB3 ATPase cycle / negative regulation by host of symbiont catalytic activity / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / small GTPase binding => GO:0031267 / Rab protein signal transduction / activation of GTPase activity / retrograde transport, endosome to Golgi / positive regulation of exocytosis ...RHOBTB3 ATPase cycle / negative regulation by host of symbiont catalytic activity / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / small GTPase binding => GO:0031267 / Rab protein signal transduction / activation of GTPase activity / retrograde transport, endosome to Golgi / positive regulation of exocytosis / phagocytic vesicle / GTPase activator activity / intracellular protein transport / cytoplasmic vesicle membrane / phagocytic vesicle membrane / GDP binding / regulation of protein localization / melanosome / protein transport / late endosome / lysosome / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / Golgi apparatus / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PH-domain like - #230 / Small G protein signalling modulator 1/2, PH domain / Small G protein signalling modulator 1/2, Rab-binding domain / Rab-binding domain (RBD) / Rab9 / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. ...PH-domain like - #230 / Small G protein signalling modulator 1/2, PH domain / Small G protein signalling modulator 1/2, Rab-binding domain / Rab-binding domain (RBD) / Rab9 / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / small GTPase Rab1 family profile. / PH-domain like / 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 nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Small G protein signaling modulator 1 / Ras-related protein Rab-9A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZhang, Z. / Wang, S. / Ding, J.
CitationJournal: Structure / Year: 2014
Title: Crystal structure of the Rab9A-RUTBC2 RBD complex reveals the molecular basis for the binding specificity of Rab9A with RUTBC2.
Authors: Zhang, Z. / Wang, S. / Shen, T. / Chen, J. / Ding, J.
History
DepositionJul 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.4Nov 8, 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_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_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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-9A
B: Small G protein signaling modulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8694
Polymers44,3222
Non-polymers5472
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-20 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.776, 59.944, 127.840
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 / Rab9A / Sid 99


Mass: 23918.771 Da / Num. of mol.: 1 / Fragment: UNP residues 1-199 / Mutation: Q66L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rab9a, Rab9, Sid99 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q9R0M6
#2: Protein Small G protein signaling modulator 1 / RUTBC2 RBD / RUN and TBC1 domain-containing protein 2


Mass: 20403.002 Da / Num. of mol.: 1 / Fragment: UNP residues 254-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sgsm1, Rutbc2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q8BPQ7
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.08 % / Mosaicity: 0.96 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M ammonium acetate, 0.1M sodium acetate, 20% (w/v) PEG 4000, pH 5.0, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionRedundancy: 5.7 % / Number: 107241 / Rmerge(I) obs: 0.079 / Χ2: 1.13 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 18655 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.955010.0440.9845.2
3.934.9510.0711.4785.3
3.443.9310.0791.3395.6
3.123.4410.0691.0135.9
2.93.1210.0871.3785.9
2.732.910.121.1355.9
2.592.7310.1571.1085.9
2.482.5910.2121.0035.9
2.382.4810.2890.9366
2.32.3810.3540.9466
ReflectionResolution: 2.3→50 Å / Num. obs: 18655 / % possible obs: 98.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.128 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.3860.35418220.946100
2.38-2.4860.28918590.936100
2.48-2.595.90.21218541.003100
2.59-2.735.90.15718661.108100
2.73-2.95.90.1218641.135100
2.9-3.125.90.08718741.37899.9
3.12-3.445.90.06918671.01399.9
3.44-3.935.60.07918961.33999.5
3.93-4.955.30.07118501.47895.8
4.95-505.20.04419030.98492.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YZL

1yzl


Resolution: 2.3→43.725 Å / FOM work R set: 0.8374 / SU ML: 0.65 / σ(F): 1.36 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 961 5.21 %random
Rwork0.1806 ---
obs0.1831 18429 98.68 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.04 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 158.17 Å2 / Biso mean: 56.33 Å2 / Biso min: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1-17.3212 Å2-0 Å2-0 Å2
2---11.0952 Å20 Å2
3----6.226 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 33 104 2696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092655
X-RAY DIFFRACTIONf_angle_d1.2163608
X-RAY DIFFRACTIONf_chiral_restr0.087389
X-RAY DIFFRACTIONf_plane_restr0.005461
X-RAY DIFFRACTIONf_dihedral_angle_d19.308966
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.42130.29791500.225124672617100
2.4213-2.57290.30441470.215224582605100
2.5729-2.77160.29961410.197624922633100
2.7716-3.05040.2411350.191624962631100
3.0504-3.49170.23191480.167825102658100
3.4917-4.39850.22321260.16692527265398
4.3985-43.73280.18341140.17592518263293
Refinement TLS params.Method: refined / Origin x: -1.8756 Å / Origin y: 19.684 Å / Origin z: -13.6395 Å
111213212223313233
T0.1879 Å2-0.003 Å2-0.0008 Å2-0.2277 Å20.035 Å2--0.2367 Å2
L1.3961 °2-0.2648 °2-0.2249 °2-2.7585 °20.6187 °2--4.0279 °2
S-0.0215 Å °0.0931 Å °0.0312 Å °-0.2117 Å °-0.0343 Å °-0.096 Å °-0.1639 Å °-0.0521 Å °0.0473 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 177
2X-RAY DIFFRACTION1allB254 - 424
3X-RAY DIFFRACTION1allA1 - 301
4X-RAY DIFFRACTION1allA1 - 302
5X-RAY DIFFRACTION1allA1 - 474

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