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- PDB-7xqv: The complex of nanobody Rh57 binding to GTP-bound RhoA active form -

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Basic information

Entry
Database: PDB / ID: 7xqv
TitleThe complex of nanobody Rh57 binding to GTP-bound RhoA active form
Components
  • Rh57
  • RhoA
KeywordsPROTEIN BINDING
Function / homologyALANINE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
Camelus bactrianus (Bactrian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsZhang, Y.R. / Liu, R. / Ding, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32070939 China
National Science Foundation (NSF, China)82030106 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural insights into the binding of nanobody Rh57 to active RhoA-GTP.
Authors: Zhang, Y. / Cheng, S. / Zhong, P. / Wang, Z. / Liu, R. / Ding, Y.
History
DepositionMay 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 8, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RhoA
B: Rh57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5425
Polymers36,9072
Non-polymers6363
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-26 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.030, 142.030, 69.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein RhoA


Mass: 20696.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli)
#2: Antibody Rh57


Mass: 16209.780 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 7 molecules

#3: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 48.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 8000; 100 mM Tris base/ Hydrochloric acid, pH 8.5; 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.76→71.01 Å / Num. obs: 9414 / % possible obs: 99.9 % / Redundancy: 25.3 % / Biso Wilson estimate: 75.51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.381 / Rpim(I) all: 0.077 / Rrim(I) all: 0.389 / Net I/σ(I): 14.9 / Num. measured all: 237878 / Scaling rejects: 2202
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.76-2.8326.53.889182006880.4430.7643.9651.2100
12.34-71.0117.80.07224081350.9990.0170.07440.599.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KMQ

1kmq


Resolution: 2.76→62.25 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 504 5.36 %
Rwork0.2199 8897 -
obs0.2228 9401 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.59 Å2 / Biso mean: 78.0749 Å2 / Biso min: 40.33 Å2
Refinement stepCycle: final / Resolution: 2.76→62.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 38 4 2246
Biso mean--78.38 62.61 -
Num. residues----279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.76-3.040.38181250.323521862311
3.04-3.480.35241410.254221642305
3.48-4.380.26491150.215222262341
4.38-62.250.22531230.195223212444

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