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- PDB-1tu4: Crystal Structure of Rab5-GDP Complex -

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Basic information

Entry
Database: PDB / ID: 1tu4
TitleCrystal Structure of Rab5-GDP Complex
ComponentsRas-related protein Rab-5A
KeywordsPROTEIN TRANSPORT / RAB5 / GTPASE
Function / homology
Function and homology information


regulation of endosome size / cytoplasmic side of early endosome membrane / postsynaptic early endosome / synaptic vesicle recycling / amyloid-beta clearance by transcytosis / modulation by host of viral process / regulation of filopodium assembly / RAB geranylgeranylation / early endosome to late endosome transport / regulation of autophagosome assembly ...regulation of endosome size / cytoplasmic side of early endosome membrane / postsynaptic early endosome / synaptic vesicle recycling / amyloid-beta clearance by transcytosis / modulation by host of viral process / regulation of filopodium assembly / RAB geranylgeranylation / early endosome to late endosome transport / regulation of autophagosome assembly / RAB GEFs exchange GTP for GDP on RABs / early phagosome / TBC/RABGAPs / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / Synthesis of PIPs at the plasma membrane / Respiratory syncytial virus (RSV) attachment and entry / endomembrane system / canonical Wnt signaling pathway / phagocytosis / phagocytic vesicle / axon terminus / ruffle / somatodendritic compartment / Prevention of phagosomal-lysosomal fusion / small monomeric GTPase / intracellular protein transport / regulation of long-term neuronal synaptic plasticity / clathrin-coated endocytic vesicle membrane / terminal bouton / receptor internalization / G protein activity / synaptic vesicle membrane / endocytosis / phagocytic vesicle membrane / GDP binding / melanosome / actin cytoskeleton / synaptic vesicle / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / early endosome membrane / early endosome / endosome membrane / endosome / membrane raft / axon / intracellular membrane-bounded organelle / GTPase activity / neuronal cell body / dendrite / GTP binding / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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-5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhu, G. / Zhai, P. / Liu, J. / Terzyan, S. / Li, G. / Zhang, X.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural basis of Rab5-Rabaptin5 interaction in endocytosis
Authors: Zhu, G. / Zhai, P. / Liu, J. / Terzyan, S. / Li, G. / Zhang, X.C.
History
DepositionJun 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-5A
B: Ras-related protein Rab-5A
C: Ras-related protein Rab-5A
D: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,92820
Polymers77,2254
Non-polymers2,70316
Water5,567309
1
A: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8083
Polymers19,3061
Non-polymers5022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0606
Polymers19,3061
Non-polymers7535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8083
Polymers19,3061
Non-polymers5022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2528
Polymers19,3061
Non-polymers9457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: Ras-related protein Rab-5A
B: Ras-related protein Rab-5A
C: Ras-related protein Rab-5A
D: Ras-related protein Rab-5A
hetero molecules

A: Ras-related protein Rab-5A
B: Ras-related protein Rab-5A
C: Ras-related protein Rab-5A
D: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,85640
Polymers154,4518
Non-polymers5,40632
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area27680 Å2
ΔGint-470 kcal/mol
Surface area49560 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-205 kcal/mol
Surface area29380 Å2
MethodPISA
7
A: Ras-related protein Rab-5A
B: Ras-related protein Rab-5A
hetero molecules

A: Ras-related protein Rab-5A
B: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,73618
Polymers77,2254
Non-polymers2,51114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area10310 Å2
ΔGint-213 kcal/mol
Surface area27840 Å2
MethodPISA
8
C: Ras-related protein Rab-5A
D: Ras-related protein Rab-5A
hetero molecules

C: Ras-related protein Rab-5A
D: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,12022
Polymers77,2254
Non-polymers2,89518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area10340 Å2
ΔGint-214 kcal/mol
Surface area28750 Å2
MethodPISA
9
C: Ras-related protein Rab-5A
D: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,06011
Polymers38,6132
Non-polymers1,4479
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-96 kcal/mol
Surface area15990 Å2
MethodPISA
10
A: Ras-related protein Rab-5A
B: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8689
Polymers38,6132
Non-polymers1,2557
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-95 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.9, 84.9, 199.9
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Ras-related protein Rab-5A


Mass: 19306.346 Da / Num. of mol.: 4 / Fragment: GTP binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB5A, RAB5 / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P20339
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, cobalt chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.9798,0.9794,0.9253
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 12, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.97941
30.92531
ReflectionResolution: 2.2→30 Å / Num. all: 42778 / Num. obs: 42778 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 32.6
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.4 / % possible all: 89.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.61 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 191036.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1200 3 %RANDOM
Rwork0.217 ---
all0.217 39796 --
obs0.217 39796 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.2548 Å2 / ksol: 0.353337 e/Å3
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1-7.75 Å28.2 Å20 Å2
2--7.75 Å20 Å2
3----15.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-6 Å
Luzzati sigma a0.41 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5202 0 148 309 5659
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.482
X-RAY DIFFRACTIONc_scangle_it3.552.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.433 89 2.9 %
Rwork0.364 2992 -
obs--72.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GDP.PARGDP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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