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- PDB-6vij: Crystal structure of mouse RABL3 in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 6vij
TitleCrystal structure of mouse RABL3 in complex with GDP
ComponentsRab-like protein 3
KeywordsIMMUNE SYSTEM / small GTPase
Function / homology
Function and homology information


regulation of protein lipidation / natural killer cell differentiation / regulation of Ras protein signal transduction / positive regulation of cilium assembly / T cell differentiation in thymus / B cell differentiation / endomembrane system / small monomeric GTPase / intracellular protein transport / G protein activity ...regulation of protein lipidation / natural killer cell differentiation / regulation of Ras protein signal transduction / positive regulation of cilium assembly / T cell differentiation in thymus / B cell differentiation / endomembrane system / small monomeric GTPase / intracellular protein transport / G protein activity / protein stabilization / centrosome / GTPase activity / GTP binding / Golgi apparatus / protein homodimerization activity
Similarity search - Function
Ras of Complex, Roc, domain of DAPkinase / Small GTPase Rab domain profile. / Rab subfamily of small GTPases / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Rab-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsSu, L. / Tomchick, D.R. / Beutler, B.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function.
Authors: Zhong, X. / Su, L. / Yang, Y. / Nair-Gill, E. / Tang, M. / Anderton, P. / Li, X. / Wang, J. / Zhan, X. / Tomchick, D.R. / Brautigam, C.A. / Moresco, E.M.Y. / Choi, J.H. / Beutler, B.
History
DepositionJan 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Rab-like protein 3
A: Rab-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3896
Polymers55,4542
Non-polymers9354
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-46 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.910, 78.203, 118.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11chain A
21(chain B and (resid 6 through 209 or resid 301 through 302))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGDPGDPchain AAB - F6 - 30235
21ARGARGPHEPHE(chain B and (resid 6 through 209 or resid 301 through 302))BA6 - 20935 - 238
22MGMGGDPGDP(chain B and (resid 6 through 209 or resid 301 through 302))BC - D301 - 302

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Components

#1: Protein Rab-like protein 3


Mass: 27726.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rabl3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D4V7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate, 12% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.007 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.947→50 Å / Num. obs: 37652 / % possible obs: 99 % / Redundancy: 17.8 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.019 / Rrim(I) all: 0.081 / Χ2: 0.952 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.9815.82.13218270.6650.5412.2010.95999.3
1.98-2.0216.61.66118620.7850.4131.7130.95299.5
2.02-2.0617.21.42818540.8440.351.4710.96699.5
2.06-2.117.81.22318570.8730.2961.2591.03799.2
2.1-2.1518.10.94118530.9340.2250.9680.97398.9
2.15-2.2180.76418550.9510.1830.7860.95399.4
2.2-2.2517.70.59518760.9680.1440.6131.02699.2
2.25-2.3116.90.45818720.9790.1130.4721.00898.8
2.31-2.3817.30.39518570.9840.0970.4070.98998.8
2.38-2.4618.80.32918820.9910.0770.3380.97599.8
2.46-2.5418.70.2718560.9920.0640.2780.98899.3
2.54-2.6518.70.21818820.9940.0510.2240.97399.1
2.65-2.7718.50.16418760.9960.0390.1690.99299.1
2.77-2.91180.1218950.9980.0290.1240.97199.1
2.91-3.1170.08418460.9980.0210.0870.98997.5
3.1-3.3319.10.06618990.9990.0150.0680.95399.9
3.33-3.6718.70.05119290.9990.0120.0530.9799.3
3.67-4.218.10.04118890.9990.010.0420.90698.1
4.2-5.2917.50.03519400.9990.0090.0360.79598.5
5.29-50170.029204510.0070.030.6997.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→42.02 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.78
RfactorNum. reflection% reflection
Rfree0.227 2000 5.74 %
Rwork0.1936 --
obs0.1955 34847 91.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.87 Å2 / Biso mean: 33.184 Å2 / Biso min: 5.84 Å2
Refinement stepCycle: final / Resolution: 1.95→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 58 208 3240
Biso mean--21.1 35.9 -
Num. residues----377
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1787X-RAY DIFFRACTION5.409TORSIONAL
12B1787X-RAY DIFFRACTION5.409TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-1.99580.2389830.2452137054
1.9958-2.04970.28631060.2258174669
2.0497-2.110.2721240.2297202380
2.11-2.17810.24441360.2094224589
2.1781-2.2560.25581490.2106243397
2.256-2.34630.24791510.2029247797
2.3463-2.45310.24221560.20212556100
2.4531-2.58240.24861530.193253299
2.5824-2.74410.25371540.2095252799
2.7441-2.9560.22221540.2068252499
2.956-3.25330.23181550.1943255199
3.2533-3.72390.2281570.1883258299
3.7239-4.69070.19041570.1602256298
4.6907-42.020.19551650.1826271999
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)
11.5106-1.25390.08963.5611-0.83441.8939-0.00550.19180.05090.17530.17070.5124-0.106-0.7253-0.180.27360.2718-0.01170.49730.05040.237-38.76585.3293-39.8935
25.2743-2.7681.69563.7889-2.81786.07870.0590.016-0.7992-0.2907-0.05490.80270.5302-0.8974-0.43540.1665-0.074-0.00230.4828-0.05270.2928-40.1191-6.3107-31.1978
33.0652-0.3879-0.17223.4908-0.32393.3912-0.08020.3568-0.1019-0.00870.0948-0.0980.09840.0468-0.02140.06790.002-0.03650.11310.00880.0596-14.4928-0.4303-18.4955
42.7361-0.12040.48534.1573-2.24043.39160.12051.16740.8286-0.1383-0.2727-0.3861-0.56450.35090.08910.2388-0.0332-0.00640.34050.0720.2639-10.58977.9607-24.6714
52.5591-2.41142.03864.1172-3.79213.94470.0289-0.0604-0.17690.0254-0.0833-0.28510.09090.06680.10350.15030.0047-0.009-0.00030.00130.314-13.0857-8.3125-19.948
62.06950.8810.34962.3174-0.05312.53030.0726-0.4955-0.11980.1709-0.1589-0.0302-0.1853-0.28860.03170.0916-0.0015-0.01990.13190.0240.1184-19.1895-0.3383-14.4007
76.38592.1517-0.9315.97940.63085.61770.0952-0.7310.45720.8628-0.09570.142-0.5475-0.75830.10910.34780.1325-0.04810.289-0.04310.1604-19.230210.1886-4.9431
84.0105-0.1731-0.32223.55960.02123.46410.023-0.78550.38540.8491-0.13580.1967-0.3242-0.0747-0.0930.2421-0.0798-0.10920.3149-0.00690.1173-13.27073.397-5.7007
97.06710.05971.28464.30050.7956.0123-0.20210.06780.35370.39870.2549-0.6821-0.45570.91780.15340.4193-0.0148-0.20220.5638-0.06410.1677-3.35447.61341.2814
103.9509-1.2092-1.24671.18090.55110.4436-0.2806-0.1412-0.20110.34030.0105-0.3805-0.01620.2067-0.02570.1174-0.0783-0.06220.25390.05780.267-3.3843-0.1199-10.5319
115.04961.35230.24394.77950.57113.1293-0.1213-0.6382-0.57330.3179-0.11020.080.5335-0.1350.03730.1808-0.0228-0.00350.15280.09160.1715-13.8541-11.29-9.3833
121.8529-0.5964-0.51832.80270.5011.9184-0.1149-0.13120.06350.1645-0.1622-0.002-0.3294-0.5532-0.03590.15840.21650.04240.1102-0.07060.058-28.47363.2954-32.7421
134.9495-2.77561.14485.3471-1.96330.72930.16880.07110.8854-0.4061-0.4315-0.5435-0.96-0.2850.04840.55380.18080.00790.2741-0.02580.2558-24.548611.7366-31.6823
147.2129-0.2295-1.15730.61090.1170.2289-0.0114-0.2279-0.1339-0.0184-0.04610.31440.2066-0.4680.0060.0441-0.01090.01790.3829-0.03050.1524-37.7259-1.4547-24.1295
150.37770.297-0.03481.4511-0.76571.92460.13990.4132-0.2354-0.5681-0.3222-0.6030.61290.5024-0.12480.31230.15680.15420.2955-0.03750.0715-21.0412-3.4314-40.4911
166.40692.202-0.01075.11552.42335.01010.10771.0504-1.8163-0.6844-0.1179-0.32640.9447-0.17940.04790.95280.05160.05110.2729-0.12010.5963-26.5585-15.0603-39.4808
171.55091.0845-0.06172.746-0.74153.1574-0.01350.99210.0476-1.0505-0.06730.5210.0673-0.7675-0.47870.45820.1631-0.11580.6525-0.04270.1713-35.16433.1632-50.1754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 171 through 190 )A171 - 190
2X-RAY DIFFRACTION2chain 'A' and (resid 191 through 209 )A191 - 209
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 28 )B2 - 28
4X-RAY DIFFRACTION4chain 'B' and (resid 29 through 41 )B29 - 41
5X-RAY DIFFRACTION5chain 'B' and (resid 42 through 50 )B42 - 50
6X-RAY DIFFRACTION6chain 'B' and (resid 51 through 99 )B51 - 99
7X-RAY DIFFRACTION7chain 'B' and (resid 100 through 114 )B100 - 114
8X-RAY DIFFRACTION8chain 'B' and (resid 115 through 153 )B115 - 153
9X-RAY DIFFRACTION9chain 'B' and (resid 154 through 170 )B154 - 170
10X-RAY DIFFRACTION10chain 'B' and (resid 171 through 190 )B171 - 190
11X-RAY DIFFRACTION11chain 'B' and (resid 191 through 210 )B191 - 210
12X-RAY DIFFRACTION12chain 'A' and (resid 6 through 28 )A6 - 28
13X-RAY DIFFRACTION13chain 'A' and (resid 29 through 41 )A29 - 41
14X-RAY DIFFRACTION14chain 'A' and (resid 42 through 66 )A42 - 66
15X-RAY DIFFRACTION15chain 'A' and (resid 67 through 112 )A67 - 112
16X-RAY DIFFRACTION16chain 'A' and (resid 113 through 140 )A113 - 140
17X-RAY DIFFRACTION17chain 'A' and (resid 141 through 170 )A141 - 170

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