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- PDB-2nzj: The crystal structure of REM1 in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 2nzj
TitleThe crystal structure of REM1 in complex with GDP
ComponentsGTP-binding protein REM 1
KeywordsSIGNALING PROTEIN / REM1 / GDP/GTP binding / GTP hydrolysis / Rad and Gem like GTP binding protein 1 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of skeletal muscle contraction by calcium ion signaling / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / I band / T-tubule / calcium channel regulator activity / transmembrane transporter binding / calmodulin binding / GTPase activity / GTP binding / plasma membrane
Similarity search - Function
Ras-related small G protein, RGK family / : / Small GTPase Ras domain profile. / 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 ...Ras-related small G protein, RGK family / : / Small GTPase Ras domain profile. / 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 / GTP-binding protein REM 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTurnbull, A.P. / Papagrigoriou, E. / Ugochukwu, E. / Elkins, J.M. / Soundararajan, M. / Yang, X. / Gorrec, F. / Umeano, C. / Salah, E. / Burgess, N. ...Turnbull, A.P. / Papagrigoriou, E. / Ugochukwu, E. / Elkins, J.M. / Soundararajan, M. / Yang, X. / Gorrec, F. / Umeano, C. / Salah, E. / Burgess, N. / Johansson, C. / Berridge, G. / Gileadi, O. / Bray, J. / Marsden, B. / Watts, S. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Sundstrom, M. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of REM1 in complex with GDP
Authors: Turnbull, A.P. / Papagrigoriou, E. / Ugochukwu, E. / Elkins, J.M. / Soundararajan, M. / Yang, X. / Gorrec, F. / Umeano, C. / Salah, E. / Burgess, N. / Johansson, C. / Berridge, G. / Gileadi, ...Authors: Turnbull, A.P. / Papagrigoriou, E. / Ugochukwu, E. / Elkins, J.M. / Soundararajan, M. / Yang, X. / Gorrec, F. / Umeano, C. / Salah, E. / Burgess, N. / Johansson, C. / Berridge, G. / Gileadi, O. / Bray, J. / Marsden, B. / Watts, S. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Sundstrom, M. / Doyle, D.
History
DepositionNov 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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: GTP-binding protein REM 1
B: GTP-binding protein REM 1
C: GTP-binding protein REM 1
D: GTP-binding protein REM 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,92114
Polymers77,9804
Non-polymers1,94110
Water28816
1
A: GTP-binding protein REM 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9984
Polymers19,4951
Non-polymers5033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein REM 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9984
Polymers19,4951
Non-polymers5033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GTP-binding protein REM 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9623
Polymers19,4951
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GTP-binding protein REM 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9623
Polymers19,4951
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: GTP-binding protein REM 1
hetero molecules

C: GTP-binding protein REM 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9607
Polymers38,9902
Non-polymers9705
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444-x-1,y-1/2,-z-1/21
Buried area3540 Å2
ΔGint-52 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.640, 102.284, 165.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
12C
22D

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111TYRTYRALAALAAA81 - 1015 - 25
211TYRTYRALAALABB81 - 1015 - 25
311TYRTYRALAALACC81 - 1015 - 25
411TYRTYRALAALADD81 - 1015 - 25
521TYRTYRTRPTRPAA117 - 13641 - 60
621TYRTYRTRPTRPBB117 - 13641 - 60
721TYRTYRTRPTRPCC117 - 13641 - 60
821TYRTYRTRPTRPDD117 - 13641 - 60
931GLYGLYGLUGLUAA154 - 17078 - 94
1031GLYGLYGLUGLUBB154 - 17078 - 94
1131GLYGLYGLUGLUCC154 - 17078 - 94
1231GLYGLYGLUGLUDD154 - 17078 - 94
1341PROPROLEULEUAA189 - 199113 - 123
1441PROPROLEULEUBB189 - 199113 - 123
1541PROPROLEULEUCC189 - 199113 - 123
1641PROPROLEULEUDD189 - 199113 - 123
1751LYSLYSARGARGAA220 - 244144 - 168
1851LYSLYSARGARGBB220 - 244144 - 168
1951LYSLYSARGARGCC220 - 244144 - 168
2051LYSLYSARGARGDD220 - 244144 - 168
112THRTHRVALVALCC182 - 188106 - 112
212THRTHRVALVALDD182 - 188106 - 112

NCS ensembles :
ID
1
2

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Components

#1: Protein
GTP-binding protein REM 1 / Rad and Gem-like GTP-binding protein 1 / GTPase-regulating endothelial cell sprouting


Mass: 19494.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REM1, GES, REM / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3/Rosetta / References: UniProt: O75628
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 34 % (w/v) PEG3350, 0.26M NaCl, 0.1 M HEPES, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 23, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 25510 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 %
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2G3Y, 2GJS, 2DPX

2g3y

2gjs

2dpx


Resolution: 2.5→29 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.894 / SU B: 21.523 / SU ML: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.564 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27988 1284 5 %RANDOM
Rwork0.2246 ---
all0.22728 24187 --
obs0.22728 24187 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.796 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---1.74 Å20 Å2
3---1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4651 0 118 16 4785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214827
X-RAY DIFFRACTIONr_bond_other_d0.0020.023087
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9876572
X-RAY DIFFRACTIONr_angle_other_deg0.92537489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6625616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77522.796186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92215743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0821541
X-RAY DIFFRACTIONr_chiral_restr0.0680.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025353
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021009
X-RAY DIFFRACTIONr_nbd_refined0.2080.2864
X-RAY DIFFRACTIONr_nbd_other0.1970.23126
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22336
X-RAY DIFFRACTIONr_nbtor_other0.0850.22588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2118
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4991.53156
X-RAY DIFFRACTIONr_mcbond_other0.0941.51294
X-RAY DIFFRACTIONr_mcangle_it0.8824913
X-RAY DIFFRACTIONr_scbond_it1.21331928
X-RAY DIFFRACTIONr_scangle_it1.8874.51659
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A554tight positional0.040.05
12B554tight positional0.040.05
13C554tight positional0.040.05
14D554tight positional0.040.05
21C42tight positional0.030.05
11A631medium positional0.240.5
12B631medium positional0.330.5
13C631medium positional0.250.5
14D631medium positional0.280.5
21C30medium positional0.610.5
11A554tight thermal0.070.5
12B554tight thermal0.080.5
13C554tight thermal0.080.5
14D554tight thermal0.070.5
21C42tight thermal0.070.5
11A631medium thermal0.382
12B631medium thermal0.412
13C631medium thermal0.412
14D631medium thermal0.382
21C30medium thermal0.262
LS refinement shellResolution: 2.5→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 99 -
Rwork0.305 1653 -
obs--92.02 %
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)
12.77543.0356-1.4763.3211-1.64481.775-0.0443-0.35240.04710.20360.02650.17610.06780.02090.01780.1769-0.0062-0.0390.1386-0.01610.1929-20.12138.5536-19.7061
22.22222.0888-1.74392.4599-0.95982.2981-0.1169-0.1458-0.1781-0.30440.06140.09330.3039-0.0030.05540.3825-0.001-0.02630.2012-0.01410.3623-20.16988.1241-24.7781
33.45880.7661-1.15143.1918-0.98484.3591-0.11160.21320.181-0.44980.15310.22180.2238-0.0714-0.04140.0694-0.0224-0.004-0.0424-0.00360.0908-16.200217.199-30.0004
43.7792-4.1289-0.42545.77821.45960.82890.21570.6322-0.2884-0.7467-0.289-0.20990.01650.17360.07330.2882-0.01630.04870.2160.00080.216-1.38187.5387-67.1037
53.6171-1.3509-2.15282.12980.44891.5704-0.19240.1203-0.55520.1231-0.0322-0.10230.23040.00220.22470.4063-0.01450.02990.2395-0.02380.3924-2.18768.1494-59.7147
63.7546-1.0868-1.33023.55730.09213.6518-0.0197-0.4050.08620.24850.0914-0.20410.17250.2141-0.07170.0929-0.01820.024-0.0555-0.03820.0892-5.869417.1766-54.4655
71.40260.34640.77664.9497-0.92120.845-0.0792-0.2707-0.19680.63830.2183-0.1282-0.0603-0.1695-0.13910.23880.031-0.00290.2343-0.04870.2093-7.270535.8734-60.16
80.1957-0.8272-0.38185.65150.27861.5731-0.05220.0968-0.2760.11210.0391-0.34340.18230.20560.01310.3910.0298-0.04970.27510.00850.3303-7.081636.017-65.5464
93.83441.6996-0.49137.57080.80242.7945-0.11580.24460.0946-0.59970.06970.26090.050.08170.04610.12580.0319-0.0183-0.0120.05990.0432-10.862845.3423-70.613
106.0176-3.52671.46277.3054-0.45654.33830.55680.1222-0.233-1.0308-0.14490.13560.3779-0.0915-0.41190.3604-0.063-0.11390.18820.01450.1801-13.711736.2788-20.8268
110.5537-0.7056-0.86938.1265-0.63992.7155-0.06950.0564-0.2993-0.4363-0.09250.26650.2587-0.21840.16190.4299-0.0396-0.02240.2966-0.01650.3117-13.986935.5745-17.1984
124.0189-2.7086-0.72410.4685-1.79643.5848-0.1408-0.22960.20030.70890.2771-0.44950.0059-0.2642-0.13620.1506-0.0323-0.06150.0037-0.04710.0281-11.491144.6339-10.9189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1102 - 34
2X-RAY DIFFRACTION2AA111 - 17235 - 96
3X-RAY DIFFRACTION3AA173 - 24897 - 172
4X-RAY DIFFRACTION4BB0 - 1112 - 35
5X-RAY DIFFRACTION5BB112 - 17136 - 95
6X-RAY DIFFRACTION6BB172 - 24896 - 172
7X-RAY DIFFRACTION7CC0 - 1112 - 35
8X-RAY DIFFRACTION8CC112 - 17136 - 95
9X-RAY DIFFRACTION9CC172 - 24796 - 171
10X-RAY DIFFRACTION10DD0 - 1112 - 35
11X-RAY DIFFRACTION11DD112 - 17036 - 94
12X-RAY DIFFRACTION12DD171 - 24695 - 170

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