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- PDB-4hlq: Crystal structure of human rab1b bound to GDP and BEF3 in complex... -

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Basic information

Entry
Database: PDB / ID: 4hlq
TitleCrystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of TBC1D20 from homo sapiens
Components
  • Ras-related protein Rab-1B
  • TBC1 domain family member 20
KeywordsHYDROLASE ACTIVATOR/PROTEIN TRANSPORT / Rab1b / RabGAP / Fluorides / GTPase-Activating Proteins / rab GTP-Binding Proteins / HYDROLASE ACTIVATOR-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


positive regulation of glycoprotein metabolic process / positive regulation of ER to Golgi vesicle-mediated transport / acrosome assembly / host-mediated activation of viral genome replication / lens fiber cell morphogenesis / COPII-coated vesicle cargo loading / phagophore assembly site membrane / RAB geranylgeranylation / regulation of autophagosome assembly / lipid droplet organization ...positive regulation of glycoprotein metabolic process / positive regulation of ER to Golgi vesicle-mediated transport / acrosome assembly / host-mediated activation of viral genome replication / lens fiber cell morphogenesis / COPII-coated vesicle cargo loading / phagophore assembly site membrane / RAB geranylgeranylation / regulation of autophagosome assembly / lipid droplet organization / RAB GEFs exchange GTP for GDP on RABs / positive regulation by virus of viral protein levels in host cell / Golgi Cisternae Pericentriolar Stack Reorganization / TBC/RABGAPs / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / seminiferous tubule development / Golgi organization / positive regulation of GTPase activity / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / COPI-mediated anterograde transport / endomembrane system / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / small monomeric GTPase / intracellular protein transport / small GTPase binding / G protein activity / nuclear membrane / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / extracellular exosome / cytosol
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1310 / GTPase-activating protein TBC20/Gyp8-like / Ypt/Rab-GAP domain of gyp1p, domain 3 / 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. / : / ARF-like small GTPases; ARF, ADP-ribosylation factor ...Helicase, Ruva Protein; domain 3 - #1310 / GTPase-activating protein TBC20/Gyp8-like / Ypt/Rab-GAP domain of gyp1p, domain 3 / 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. / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. / Cyclin A; domain 1 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Helicase, Ruva Protein; domain 3 / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / GUANOSINE-5'-DIPHOSPHATE / TBC1 domain family member 20 / Ras-related protein Rab-1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGazdag, E.M. / Gavriljuk, K. / Itzen, A. / Koetting, C. / Gerwert, K. / Goody, R.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Catalytic mechanism of a mammalian Rab-RabGAP complex in atomic detail.
Authors: Gavriljuk, K. / Gazdag, E.M. / Itzen, A. / Kotting, C. / Goody, R.S. / Gerwert, K.
History
DepositionOct 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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.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_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: TBC1 domain family member 20
B: Ras-related protein Rab-1B
C: TBC1 domain family member 20
D: Ras-related protein Rab-1B
E: TBC1 domain family member 20
F: Ras-related protein Rab-1B
G: TBC1 domain family member 20
H: Ras-related protein Rab-1B
I: TBC1 domain family member 20
J: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,72530
Polymers273,57710
Non-polymers3,14820
Water91951
1
A: TBC1 domain family member 20
B: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3456
Polymers54,7152
Non-polymers6304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-34 kcal/mol
Surface area19770 Å2
MethodPISA
2
C: TBC1 domain family member 20
D: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3456
Polymers54,7152
Non-polymers6304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-38 kcal/mol
Surface area19710 Å2
MethodPISA
3
E: TBC1 domain family member 20
F: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4417
Polymers54,7152
Non-polymers7265
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-40 kcal/mol
Surface area20080 Å2
MethodPISA
4
G: TBC1 domain family member 20
H: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2495
Polymers54,7152
Non-polymers5343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-26 kcal/mol
Surface area20320 Å2
MethodPISA
5
I: TBC1 domain family member 20
J: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3456
Polymers54,7152
Non-polymers6304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-43 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.170, 118.640, 290.110
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 , 2 types, 10 molecules ACEGIBDFHJ

#1: Protein
TBC1 domain family member 20


Mass: 34963.113 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D20, C20orf140 / Plasmid: pOPINM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q96BZ9
#2: Protein
Ras-related protein Rab-1B


Mass: 19752.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1B / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9H0U4

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Non-polymers , 5 types, 71 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: BeF3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 1.6M ammonium sulphate, 0.1M Hepes pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2012
RadiationMonochromator: SI(111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 46667 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.63 % / Rmerge(I) obs: 0.0561 / Rsym value: 0.0695 / Net I/σ(I): 3.31
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 6.47 % / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERMRphasing
REFMAC5.5.0070refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HL4, 3NKV

4hl4

3nkv


Resolution: 3.3→49.22 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.874 / SU B: 57.698 / SU ML: 0.448 / Cross valid method: THROUGHOUT / ESU R Free: 0.583 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27432 2334 5 %RANDOM
Rwork0.206 ---
obs0.20937 46667 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.194 Å2
Baniso -1Baniso -2Baniso -3
1-4.05 Å20 Å20 Å2
2---2.67 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 3.3→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17524 0 190 51 17765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02218082
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.97124652
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.10152249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29824.084813
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.112152848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.18215105
X-RAY DIFFRACTIONr_chiral_restr0.0730.22829
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023646
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1981.511277
X-RAY DIFFRACTIONr_mcbond_other0.0571.54516
X-RAY DIFFRACTIONr_mcangle_it0.386218056
X-RAY DIFFRACTIONr_scbond_it0.50636805
X-RAY DIFFRACTIONr_scangle_it0.9064.56596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 169 -
Rwork0.26 3210 -
obs--100 %
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)
10.9851-0.1981-0.11152.77180.60572.6451-0.0717-0.12240.03420.20840.0325-0.13520.10840.27220.03920.0354-0.00240.01780.15120.03470.107-8.042113.9756-60.2682
22.9816-0.08650.29853.74490.24463.42110.02410.17870.2675-0.45010.03750.0134-0.3620.0303-0.06160.1701-0.03530.0550.16160.03680.1214-8.030618.395-90.848
32.87390.0998-0.01051.3119-0.1151.6920.0120.1247-0.1237-0.1108-0.1052-0.02510.20030.01950.09320.1579-0.01820.09990.06530.00260.142115.276542.4196-54.8228
43.4407-0.15750.71812.60580.24662.71380.1072-0.4488-0.110.3748-0.11410.04020.0129-0.33470.00680.3325-0.07250.11270.29710.05490.16512.889340.3077-24.169
51.9380.1202-0.43411.8868-0.23672.4114-0.0072-0.0464-0.070.37640.03720.25590.1081-0.2648-0.03010.24910.03030.06860.12720.04870.1808-38.347711.1559-29.3164
62.51160.109-0.12023.1148-0.02852.34520.01340.3481-0.2602-0.1892-0.04010.23170.1723-0.26410.02660.10340.02610.02510.3242-0.0220.2305-43.981912.076-59.8205
71.8861-0.40591.16041.6006-0.44862.95290.3543-0.2196-0.23680.1067-0.0264-0.04440.6309-0.1362-0.32790.8612-0.138-0.03860.18190.11320.3867-24.9401-19.1941-1.4629
82.82770.0430.80882.9795-0.59492.94780.35390.4-0.430.0335-0.0563-0.15931.10060.2516-0.29761.13130.0969-0.12290.2456-0.0290.4174-26.99-22.0014-31.9146
91.0378-0.2591-0.14582.53130.18893.1202-0.04230.08220.20280.1845-0.0058-0.1331-0.41890.11560.04820.2064-0.0228-0.03640.17810.07340.2883-44.039257.3523-26.4728
103.39660.0752-0.37251.74780.97883.4674-0.0592-0.32220.02990.43830.1172-0.25360.04820.507-0.0580.6260.0088-0.12750.33120.0390.3141-41.525556.03464.1453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 304
2X-RAY DIFFRACTION2B3 - 174
3X-RAY DIFFRACTION3C25 - 305
4X-RAY DIFFRACTION4D4 - 173
5X-RAY DIFFRACTION5E25 - 305
6X-RAY DIFFRACTION6F3 - 174
7X-RAY DIFFRACTION7G25 - 305
8X-RAY DIFFRACTION8H4 - 173
9X-RAY DIFFRACTION9I25 - 305
10X-RAY DIFFRACTION10J4 - 174

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