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- PDB-2fol: Crystal structure of human RAB1A in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 2fol
TitleCrystal structure of human RAB1A in complex with GDP
ComponentsRas-related protein Rab-1A
KeywordsPROTEIN TRANSPORT / G-PROTEIN / RAB / GTP ANALOGUE / STRUCTURAL GENOMICS / STRUCT URAL GENOMICS CONSORTIUM / SGC / Structural Genomics Consortium
Function / homology
Function and homology information


positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic ...positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / transport vesicle membrane / Golgi organization / autophagosome assembly / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / vesicle-mediated transport / substrate adhesion-dependent cell spreading / small monomeric GTPase / positive regulation of interleukin-8 production / intracellular protein transport / G protein activity / autophagy / endocytosis / melanosome / cell migration / early endosome / defense response to bacterium / cadherin binding / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome / cytosol
Similarity search - Function
: / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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 ...: / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.631 Å
AuthorsWang, J. / Tempel, W. / Shen, Y. / Shen, L. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
Citation
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Real-Space Protein-Model Completion: an Inverse-Kinematics Approach.
Authors: van den Bedem, H. / Lotan, I. / Latombe, J.-C. / Deacon, A.M.
History
DepositionJan 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 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 1.4Aug 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 / 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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH ...BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.
Remark 42MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REFERENCE : NEW TOOLS AND DATA FOR IMPROVING : STRUCTURES, USING ALL-ATOM CONTACTS : METHODS IN ENZYMOLOGY. 2003;374:385-412. MOLPROBITY OUTPUT SCORES: ALL-ATOM CLASHSCORE : 18.17 (0.00 B<40) BAD ROTAMERS : 6.6% 9/137 (TARGET 0-1%) RAMACHANDRAN OUTLIERS : 0.0% 0/151 (TARGET 0.2%) RAMACHANDRAN FAVORED : 95.4% 144/151 (TARGET 98.0%)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0355
Polymers21,5671
Non-polymers4684
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.790, 75.790, 49.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-401-

UNX

Detailsnot known

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Components

#1: Protein Ras-related protein Rab-1A / YPT1-related protein


Mass: 21567.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1A, RAB1 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: P62820
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG3350, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.62→30 Å / Num. obs: 5102 / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.088 / Χ2: 1.022
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsΧ2Diffraction-ID
2.62-2.7110010.50.8264940.5441
2.71-2.8210010.70.6445090.511
2.82-2.9510010.80.4234930.581
2.95-3.1110010.80.2885020.6441
3.11-3.310010.80.2015090.7661
3.3-3.5510010.80.1355001.0041
3.55-3.9110010.70.0975081.3211
3.91-4.4810010.70.0675181.4871
4.48-5.6310010.60.0555191.6331
5.63-3099.8100.0345501.6891

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1YZN, 1UKV

1yzn

1ukv


Resolution: 2.631→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.167 / SU B: 32.488 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R Free: 0.347 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2523 233 4.616 %
Rwork0.199 --
all0.201 --
obs-5048 99.98 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.747 Å2
Baniso -1Baniso -2Baniso -3
1--0.603 Å2-0.302 Å20 Å2
2---0.603 Å20 Å2
3---0.905 Å2
Refinement stepCycle: LAST / Resolution: 2.631→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 31 5 1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221289
X-RAY DIFFRACTIONr_bond_other_d0.0020.02852
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9881745
X-RAY DIFFRACTIONr_angle_other_deg0.79732087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7545153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0225.08857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05215235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.925155
X-RAY DIFFRACTIONr_chiral_restr0.0750.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02257
X-RAY DIFFRACTIONr_nbd_refined0.2230.3302
X-RAY DIFFRACTIONr_nbd_other0.2090.3879
X-RAY DIFFRACTIONr_nbtor_refined0.1910.5615
X-RAY DIFFRACTIONr_nbtor_other0.0970.5655
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.566
X-RAY DIFFRACTIONr_metal_ion_refined0.1370.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.326
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.52
X-RAY DIFFRACTIONr_mcbond_it0.4591.5994
X-RAY DIFFRACTIONr_mcbond_other0.0691.5317
X-RAY DIFFRACTIONr_mcangle_it0.59921237
X-RAY DIFFRACTIONr_mcangle_other0.26821019
X-RAY DIFFRACTIONr_scbond_it0.993640
X-RAY DIFFRACTIONr_scbond_other0.2873766
X-RAY DIFFRACTIONr_scangle_it1.6624.5508
X-RAY DIFFRACTIONr_scangle_other0.7534.51068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.631-2.6990.396130.4063560.405369100
2.699-2.7720.251180.3423240.337342100
2.772-2.8520.282140.3363430.334357100
2.852-2.9380.278180.3043120.303330100
2.938-3.0340.301200.2633150.265335100
3.034-3.1390.407180.2762920.284310100
3.139-3.2560.22580.252930.249301100
3.256-3.3880.213130.2042770.204290100
3.388-3.5360.256130.2192760.221289100
3.536-3.7060.322130.2012580.207271100
3.706-3.9030.245150.1882490.191264100
3.903-4.1360.185100.1832410.183251100
4.136-4.4150.173120.142100.142222100
4.415-4.7610.183130.1272140.131227100
4.761-5.2020.3190.1581840.165193100
5.202-5.7940.27590.1731780.178187100
5.794-6.6490.28870.1671590.171166100
6.649-8.0460.27550.1861400.189145100
8.046-10.990.3430.1221160.124119100
10.99-300.01520.216780.2118198.765
Refinement TLS params.Method: refined / Origin x: -20.8949 Å / Origin y: 16.5437 Å / Origin z: 5.9051 Å
111213212223313233
T0.1055 Å2-0.074 Å2-0.0405 Å2-0.148 Å2-0.1592 Å2--0.0975 Å2
L3.6219 °2-0.2086 °2-0.2542 °2-3.4933 °2-1.0124 °2--1.2636 °2
S-0.0599 Å °0.5078 Å °-0.3102 Å °-0.0694 Å °0.1536 Å °-0.1911 Å °-0.0182 Å °0.0678 Å °-0.0937 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth asym-ID: A

IDLabel asym-IDAuth seq-IDLabel seq-ID
1A5 - 17322 - 190
2C - B201 - 2021

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