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- PDB-6sge: Crystal structure of Human RHOB-GTP in complex with nanobody B6 -

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Basic information

Entry
Database: PDB / ID: 6sge
TitleCrystal structure of Human RHOB-GTP in complex with nanobody B6
Components
  • Nanobody B6
  • Rho-related GTP-binding protein RhoB
KeywordsIMMUNE SYSTEM / GTPase / RHO / antibody / complex
Function / homology
Function and homology information


RHO GTPases Activate Rhotekin and Rhophilins / endothelial tube morphogenesis / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / RHOB GTPase cycle / endosome to lysosome transport / cleavage furrow / Rho protein signal transduction ...RHO GTPases Activate Rhotekin and Rhophilins / endothelial tube morphogenesis / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / RHOB GTPase cycle / endosome to lysosome transport / cleavage furrow / Rho protein signal transduction / negative regulation of cell cycle / mitotic cytokinesis / RHO GTPases activate PKNs / GPVI-mediated activation cascade / regulation of cell migration / positive regulation of endothelial cell migration / negative regulation of cell migration / actin filament organization / RHO GTPases Activate Formins / cellular response to ionizing radiation / intracellular protein transport / Schaffer collateral - CA1 synapse / cellular response to hydrogen peroxide / positive regulation of angiogenesis / GDP binding / G alpha (12/13) signalling events / late endosome membrane / angiogenesis / early endosome / cell differentiation / endosome membrane / cell adhesion / positive regulation of apoptotic process / focal adhesion / GTPase activity / GTP binding / apoptotic process / protein kinase binding / signal transduction / extracellular exosome / nucleus / plasma membrane / cytosol
Similarity search - Function
Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Immunoglobulin V-Type / Rab subfamily of small GTPases / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Immunoglobulin V-Type / Rab subfamily of small GTPases / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Small GTP-binding protein domain / Immunoglobulin subtype / Immunoglobulin / P-loop containing nucleotide triphosphate hydrolases / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / AEP5A5 / Rho-related GTP-binding protein RhoB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSoulie, S. / Gence, R. / Cabantous, S. / Lajoie-Mazenc, I. / Favre, G. / Pedelacq, J.D.
CitationJournal: Cell Chem Biol / Year: 2019
Title: A Targeted Protein Degradation Cell-Based Screening for Nanobodies Selective toward the Cellular RHOB GTP-Bound Conformation.
Authors: Bery, N. / Keller, L. / Soulie, M. / Gence, R. / Iscache, A.L. / Cherier, J. / Cabantous, S. / Sordet, O. / Lajoie-Mazenc, I. / Pedelacq, J.D. / Favre, G. / Olichon, A.
History
DepositionAug 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 24, 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho-related GTP-binding protein RhoB
B: Nanobody B6
C: Rho-related GTP-binding protein RhoB
D: Nanobody B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,18210
Polymers71,0384
Non-polymers1,1446
Water12,214678
1
A: Rho-related GTP-binding protein RhoB
B: Nanobody B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0915
Polymers35,5192
Non-polymers5723
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-34 kcal/mol
Surface area14770 Å2
MethodPISA
2
C: Rho-related GTP-binding protein RhoB
D: Nanobody B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0915
Polymers35,5192
Non-polymers5723
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-36 kcal/mol
Surface area16000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.840, 70.227, 71.212
Angle α, β, γ (deg.)90.000, 107.680, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Rho-related GTP-binding protein RhoB / Rho cDNA clone 6 / h6


Mass: 20814.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOB, ARH6, ARHB / Production host: Escherichia coli (E. coli) / References: UniProt: P62745
#2: Antibody Nanobody B6


Mass: 14704.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4E0W6L3
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 46.21 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: 100 mM Mes pH 6.5 200 mM MgCl2 25% v/w PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.3→48.795 Å / Num. obs: 110991 / % possible obs: 72.5 % / Redundancy: 2.81 % / Biso Wilson estimate: 24.866 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rrim(I) all: 0.035 / Χ2: 0.988 / Net I/σ(I): 17.39 / Num. measured all: 311846
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.381.4491.0450.6144082467230420.4511.45912.3
1.38-1.481.790.6881.02171482317595780.6920.94241.3
1.48-1.592.2140.3022.473584721624161910.9280.39174.9
1.59-1.753.0570.1695.385832219890190810.9780.20495.9
1.75-1.953.050.08810.415454818028178830.9930.10799.2
1.95-2.253.1650.04221.374999915928157950.9980.05199.2
2.25-2.763.0870.02732.614131613480133820.9990.03399.3
2.76-3.93.1750.01948.453275310481103170.9990.02398.4
3.9-48.7953.0590.01955.217505588557220.9990.02497.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDS3.2data reduction
XDS3.2data scaling
PHENIX1.16-3549phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FV8

2fv8


Resolution: 1.5→47.175 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 1710 1.79 %
Rwork0.161 93641 -
obs0.1615 95351 94.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.17 Å2 / Biso mean: 33.2646 Å2 / Biso min: 12.74 Å2
Refinement stepCycle: final / Resolution: 1.5→47.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 94 678 5630
Biso mean--18.9 39.09 -
Num. residues----620
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.54410.28311120.2502581871
1.5441-1.5940.2662117703386
1.594-1.6510.2449142763194
1.651-1.71710.2473151795197
1.7171-1.79520.2256147813499
1.7952-1.88990.2279148816599
1.8899-2.00830.2111150805499
2.0083-2.16330.1845157817099
2.1633-2.3810.1785146818299
2.381-2.72550.1887141815499
2.7255-3.43370.1886150814499
3.4337-47.1750.15771490.1424820598
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)
12.4546-0.37030.3843.06610.07676.7492-0.0067-0.2593-0.24910.2022-0.07210.00530.1813-0.27480.10840.0873-0.0145-0.01840.14590.03840.18148.754910.973685.87
22.7516-0.82521.61622.0585-2.32956.04820.1748-0.1273-0.60380.06150.02220.01790.6403-0.0662-0.21790.2203-0.0349-0.06410.14420.0410.29145.92896.51482.614
33.5749-0.0377-0.06110.8740.28382.06250.0205-0.12990.26610.05950.00190.01-0.1868-0.1241-0.03820.17720.0073-0.02150.11740.02310.180650.264420.217584.3882
43.79030.74791.41051.5774-0.93446.49590.00880.9134-0.0455-0.11920.0002-0.18260.29610.8642-0.03350.14950.0512-0.01960.39320.00080.223964.7119.718367.3039
53.0447-0.28181.05351.98842.12164.8759-0.13880.43290.1784-0.05310.1166-0.1644-0.33090.54020.02770.1545-0.0597-0.01020.22760.06670.228466.745120.586276.7441
62.62340.287-0.05422.62170.85162.8526-0.0048-0.203-0.14410.1629-0.0138-0.04630.11690.04370.01990.15980.011-0.04250.14570.03270.171958.915210.393789.3391
72.82751.18970.77796.4769-1.60873.55990.48210.4015-0.06080.4098-0.5537-0.3944-0.12660.87080.14780.28450.07350.07670.6248-0.04840.277560.827915.076648.2498
85.56831.084-0.17325.3924-1.29642.93120.15310.1711-1.0687-0.2308-0.1939-0.37110.43380.45510.1170.25530.0897-0.03780.3893-0.09020.284850.92285.832350.2028
94.8275.82665.22238.25464.99427.22220.1721-0.39410.11820.1909-0.2522-0.234-0.0622-0.09150.16890.18830.00660.00030.4001-0.00970.264954.485220.977456.2767
106.1751.0046-0.83622.5888-0.66723.71290.13610.53070.1416-0.1605-0.1401-0.05650.00930.38620.00170.15560.04890.01440.30580.00670.134146.421618.786645.3151
118.0446-0.46610.12147.7286-1.37826.11450.21651.1772-1.1621-1.0327-0.2020.18690.8810.6619-0.0390.3610.1554-0.00920.5644-0.15280.330152.7898.908742.1528
125.831.96710.48992.9159-0.29546.99780.13130.66940.577-0.05560.0084-0.0241-0.56390.6357-0.1320.16550.01290.03060.41640.04520.268657.663121.736449.5741
134.12054.8983-1.22386.1987-0.4633.0055-0.0148-0.960.55550.20540.1081-0.0285-0.06430.5485-0.20570.19630.0348-0.03270.3829-0.04070.259244.920313.999960.4626
145.74474.2746-2.24218.0375-1.09042.4863-0.19460.591-0.1492-0.1867-0.10180.3022-0.0335-0.24340.16940.15730.0145-0.07630.3146-0.00910.192254.171212.661863.6021
155.1851-2.6287-4.14132.83391.73873.39590.06431.2390.7703-0.01110.1949-0.4412-0.69510.3717-0.30140.2867-0.1274-0.00720.68610.1310.388966.404823.287648.4806
163.00011.82411.23123.35390.82992.03190.11350.5379-0.3415-0.55490.1864-0.11910.0670.6610.07990.20650.0674-0.03980.2208-0.06260.16230.759616.004239.9197
172.1258-0.42580.01930.59190.26182.91070.11580.0778-0.4232-0.02580.01340.09410.57740.0275-0.16580.24310.008-0.04390.1187-0.00640.225328.73519.806752.4606
183.76442.20055.07232.32592.88746.91930.28170.3961-0.3316-0.2934-0.0190.05010.2885-0.0215-0.33780.23670.0469-0.05680.2234-0.06670.219828.711812.807540.0054
195.02460.7216-2.04311.7075-0.67432.86950.1771-0.32580.16150.1214-0.0318-0.0504-0.05210.2501-0.14720.1633-0.0012-0.00990.1087-0.04070.166230.866922.430653.6961
208.04733.6817-4.18975.6732-5.14076.5406-0.0504-0.08520.35080.09750.12040.0812-0.2412-0.0343-0.11520.1884-0.0001-0.01310.0938-0.02710.174125.058429.397155.3695
212.41160.6818-1.9371.0526-1.76838.27180.035-0.3089-0.11180.02510.06420.13570.0217-0.4586-0.07210.11520.0006-0.02740.19450.03270.191116.153517.7260.1869
223.085-0.2176-0.04312.3168-1.41894.57820.106-0.1676-0.0526-0.12620.00560.2345-0.102-0.3929-0.12410.0828-0.0173-0.02170.1790.02230.180113.418420.649253.8466
235.88781.2197-2.20146.7161-2.6141.99320.05060.60550.0608-0.77120.13490.29560.31-0.3659-0.11120.24420.0051-0.05270.2124-0.06680.171120.866917.81537.1155
244.6451-1.56091.18363.6506-0.83990.40410.2173-0.6254-0.1282-0.2916-0.11530.3010.0732-0.4689-0.08720.2664-0.09960.02030.57550.09960.225616.736517.288986.4554
256.69891.65030.50032.4779-2.21352.7178-0.06230.1831-1.53730.06270.17960.09480.7741-0.79660.37020.3287-0.1783-0.04190.55670.11280.397824.86366.695583.9563
267.4303-4.21895.41813.6368-5.0438.8303-0.08230.03560.2902-0.0391-0.0406-0.1672-0.3602-0.05960.15750.21830.00850.0180.36280.04570.219324.097922.479578.6127
274.699-1.6571-0.47232.43860.90634.6574-0.0604-0.81860.17540.17370.06020.07320.0674-0.5791-0.03210.1624-0.0079-00.42520.02420.173431.46418.487589.5149
288.6537-1.5205-0.27511.10510.6016.4233-0.1726-0.8645-1.17890.74580.13620.2460.7917-0.47580.32350.3285-0.11560.02140.75560.18570.334823.32099.445892.244
294.0739-3.2762-0.74293.55820.87572.36410.0619-0.62870.39280.14690.0449-0.2305-0.1736-0.1483-0.0510.1769-0.0440.0220.5124-0.01330.254720.924423.462985.5124
305.7914-3.14135.69041.7181-3.03995.83710.03591.79060.2799-0.19670.1296-0.13350.10530.3643-0.16590.1917-0.0484-0.00850.52670.0770.245132.433814.367274.0381
312.779-1.347-3.56581.36981.69375.0991-0.0473-0.3530.09350.18190-0.07870.0798-0.01650.01790.2476-0.0116-0.06460.5250.04720.28415.317418.873680.8648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 27 )A3 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 48 )A28 - 48
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 117 )A49 - 117
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 133 )A118 - 133
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 151 )A134 - 151
6X-RAY DIFFRACTION6chain 'A' and (resid 152 through 180 )A152 - 180
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 17 )B1 - 17
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 33 )B18 - 33
9X-RAY DIFFRACTION9chain 'B' and (resid 34 through 45 )B34 - 45
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 73 )B46 - 73
11X-RAY DIFFRACTION11chain 'B' and (resid 74 through 84 )B74 - 84
12X-RAY DIFFRACTION12chain 'B' and (resid 85 through 99 )B85 - 99
13X-RAY DIFFRACTION13chain 'B' and (resid 100 through 105 )B100 - 105
14X-RAY DIFFRACTION14chain 'B' and (resid 106 through 118 )B106 - 118
15X-RAY DIFFRACTION15chain 'B' and (resid 119 through 126 )B119 - 126
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 11 )C2 - 11
17X-RAY DIFFRACTION17chain 'C' and (resid 12 through 48 )C12 - 48
18X-RAY DIFFRACTION18chain 'C' and (resid 49 through 60 )C49 - 60
19X-RAY DIFFRACTION19chain 'C' and (resid 61 through 88 )C61 - 88
20X-RAY DIFFRACTION20chain 'C' and (resid 89 through 106 )C89 - 106
21X-RAY DIFFRACTION21chain 'C' and (resid 107 through 134 )C107 - 134
22X-RAY DIFFRACTION22chain 'C' and (resid 135 through 166 )C135 - 166
23X-RAY DIFFRACTION23chain 'C' and (resid 167 through 184 )C167 - 184
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 17 )D1 - 17
25X-RAY DIFFRACTION25chain 'D' and (resid 18 through 33 )D18 - 33
26X-RAY DIFFRACTION26chain 'D' and (resid 34 through 45 )D34 - 45
27X-RAY DIFFRACTION27chain 'D' and (resid 46 through 73 )D46 - 73
28X-RAY DIFFRACTION28chain 'D' and (resid 74 through 84 )D74 - 84
29X-RAY DIFFRACTION29chain 'D' and (resid 85 through 99 )D85 - 99
30X-RAY DIFFRACTION30chain 'D' and (resid 100 through 105 )D100 - 105
31X-RAY DIFFRACTION31chain 'D' and (resid 106 through 134 )D106 - 134

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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