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- PDB-6vii: Crystal structure of mouse RABL3 in complex with GTPgammaS -

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Basic information

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


regulation of protein lipidation / regulation of Ras protein signal transduction / natural killer cell differentiation / endomembrane system / B cell differentiation / intracellular protein transport / T cell differentiation in thymus / protein stabilization / GTPase activity / GTP binding / protein homodimerization activity
Similarity search - Function
Ras of Complex, Roc, domain of DAPkinase / small GTPase Rab1 family profile. / Rab subfamily of small GTPases / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Rab-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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 / 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 / _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)56,5816
Polymers55,4542
Non-polymers1,1274
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rab-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2913
Polymers27,7271
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Rab-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2913
Polymers27,7271
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.506, 81.175, 109.172
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
11(chain A and (resid 4 through 71 or resid 78 through 302))
21(chain B and (resid 4 through 116 or resid 137 or resid 139 through 208 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
11LEULEUVALVAL(chain A and (resid 4 through 71 or resid 78 through 302))AB4 - 7133 - 100
12LYSLYSGSPGSP(chain A and (resid 4 through 71 or resid 78 through 302))AB - F78 - 302107
21LEULEUARGARG(chain B and (resid 4 through 116 or resid 137 or resid 139 through 208 or resid 301 through 302))BA4 - 11633 - 145
22ASPASPASPASP(chain B and (resid 4 through 116 or resid 137 or resid 139 through 208 or resid 301 through 302))BA137166
23GLNGLNTYRTYR(chain B and (resid 4 through 116 or resid 137 or resid 139 through 208 or resid 301 through 302))BA139 - 208168 - 237
24MGMGGSPGSP(chain B and (resid 4 through 116 or resid 137 or resid 139 through 208 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-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.6 M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.992→50 Å / Num. obs: 36727 / % possible obs: 99.7 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.015 / Rrim(I) all: 0.056 / Χ2: 0.946 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0392.35417780.4370.7672.4830.94798.1
2.03-2.079.42.43317980.5370.8022.5680.96699.5
2.07-2.1112.21.96318000.7510.5712.0460.95899.8
2.11-2.1513.31.37818190.9280.3851.4310.96799.8
2.15-2.213.71.19918140.9050.3321.2450.966100
2.2-2.2513.80.88918170.9280.2460.9230.98599.9
2.25-2.3113.50.63817970.9680.1780.6620.99599.7
2.31-2.3713.40.50918110.9760.1430.5290.983100
2.37-2.4413.10.39618330.9810.1120.4121.0199.9
2.44-2.5211.90.30718130.9890.0920.3211.00399.6
2.52-2.6113.90.23718330.9920.0650.2460.99799.8
2.61-2.7113.80.16718330.9950.0460.1740.98499.9
2.71-2.8413.70.12118300.9970.0340.1260.985100
2.84-2.9913.60.08418330.9980.0230.0870.97799.8
2.99-3.1713.10.0618350.9980.0170.0620.91699.9
3.17-3.4212.80.04818390.9990.0140.050.97599.6
3.42-3.7613.90.03918700.9990.0110.040.905100
3.76-4.3113.40.03518690.9990.010.0360.85199.9
4.31-5.4312.50.03218980.9990.0090.0330.77199.7
5.43-5012.40.03520070.9970.0110.0370.79199.7

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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: 2→47.992 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.56
RfactorNum. reflection% reflection
Rfree0.2283 1999 6.32 %
Rwork0.1935 --
obs0.1957 31639 85.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.18 Å2 / Biso mean: 39.9317 Å2 / Biso min: 10.62 Å2
Refinement stepCycle: final / Resolution: 2→47.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 66 151 3180
Biso mean--30.55 41.23 -
Num. residues----373
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1670X-RAY DIFFRACTION11.14TORSIONAL
12B1670X-RAY DIFFRACTION11.14TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.04180.2957380.266356823
2.0418-2.0970.3741620.246792238
2.097-2.15870.29331030.2323152763
2.1587-2.22840.26471340.2208198282
2.2284-2.3080.24911540.2143229294
2.308-2.40040.23791640.2101243099
2.4004-2.50970.2461630.20052422100
2.5097-2.6420.26741650.2032450100
2.642-2.80750.24321670.20642467100
2.8075-3.02420.24931670.19832463100
3.0242-3.32850.23181660.19582464100
3.3285-3.810.20871680.1862497100
3.81-4.79950.18721700.16012520100
4.7995-47.9920.21071780.1912636100
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)
14.324-0.70110.25253.0299-0.43145.2655-0.1406-0.79110.54010.1928-0.0588-0.1943-0.7237-0.17180.10750.21840.0336-0.0040.23590.01720.1754-1.02835.752-27.3296
22.84982.691-2.22924.3429-1.01172.5663-0.1276-0.23710.01530.08820.09440.19060.0979-0.21220.09820.1068-0.01710.01590.39130.10620.1615-7.3815-3.091-20.0308
32.8655-0.2116-1.22531.9858-1.03095.301-0.0510.0037-0.0176-0.47630.0581-0.21520.20720.64280.14340.3063-0.00410.07540.21540.030.15882.6029-2.1685-38.4861
43.66180.5848-0.71215.68-0.56514.3979-0.14160.6739-0.1146-0.9356-0.01330.16690.2255-0.74510.10060.3739-0.0409-0.02190.30160.02720.2141-9.77860.8811-40.5223
55.9358-1.7952-0.2117.6904-1.24656.002-0.0662-0.185-0.759-0.39570.02360.73810.9294-0.529-0.13480.246-0.12850.00060.27170.11470.2591-12.4446-7.7448-26.3155
63.10331.84041.27525.29080.20843.8461-0.16850.39730.0968-0.08140.05490.1552-0.1711-0.04050.1180.0927-0.0466-0.00460.22110.01090.142214.691-1.1193-18.3699
77.71510.3242-1.50524.5489-0.82163.50750.02120.77790.791-0.5777-0.1644-0.0183-0.99080.3504-0.02670.4039-0.1266-0.06590.47560.10590.233516.91068.5561-24.0313
83.0407-0.68760.40918.2780.21883.28490.06670.4591-0.3433-0.165-0.0586-0.59330.41390.12170.06680.1223-0.02420.00410.1939-0.02670.250615.915-12.4104-20.9541
94.15781.32463.2021.8858-0.17095.8821-0.2397-0.56490.80710.3914-0.23420.3057-0.9631-1.1102-0.07750.2915-0.02790.03720.2974-0.08450.2719.41754.707-9.7986
107.84930.73453.86053.1437-0.74558.2890.0434-0.99950.67670.7341-0.2910.294-0.8933-1.06970.37940.4494-0.00230.04430.3925-0.10840.256113.40816.8064-2.6777
112.5682-0.63050.91362.0348-0.723.13410.0969-0.08480.55050.5373-0.27430.1331-0.47450.0607-0.37910.2878-0.3680.04270.19560.16880.106919.87932.5578-8.2766
127.44611.8877-2.35463.055-1.1921.4608-0.13170.29220.70910.02140.1112-0.2716-0.38060.73050.18820.4839-0.2881-0.13210.58720.06850.193230.04865.4056-0.7973
132.5194-0.44271.05993.71930.9810.84940.04950.4329-0.1614-0.1077-0.0866-0.70490.03590.44770.01560.1971-0.1261-0.0280.36120.0410.281327.5528-0.8353-14.1073
148.90444.8059-2.70562.7683-0.97745.8650.2663-0.1717-0.66090.4793-0.1853-0.2850.5845-0.0227-0.01140.1946-0.0489-0.05560.12930.00790.254119.4941-11.6932-12.3304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 4 through 39 )B4 - 39
2X-RAY DIFFRACTION2chain 'B' and (resid 40 through 68 )B40 - 68
3X-RAY DIFFRACTION3chain 'B' and (resid 69 through 114 )B69 - 114
4X-RAY DIFFRACTION4chain 'B' and (resid 115 through 190 )B115 - 190
5X-RAY DIFFRACTION5chain 'B' and (resid 191 through 210 )B191 - 210
6X-RAY DIFFRACTION6chain 'A' and (resid 2 through 28 )A2 - 28
7X-RAY DIFFRACTION7chain 'A' and (resid 29 through 41 )A29 - 41
8X-RAY DIFFRACTION8chain 'A' and (resid 42 through 66 )A42 - 66
9X-RAY DIFFRACTION9chain 'A' and (resid 67 through 99 )A67 - 99
10X-RAY DIFFRACTION10chain 'A' and (resid 100 through 114 )A100 - 114
11X-RAY DIFFRACTION11chain 'A' and (resid 115 through 153 )A115 - 153
12X-RAY DIFFRACTION12chain 'A' and (resid 154 through 170 )A154 - 170
13X-RAY DIFFRACTION13chain 'A' and (resid 171 through 190 )A171 - 190
14X-RAY DIFFRACTION14chain 'A' and (resid 191 through 208 )A191 - 208

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