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- PDB-8im0: mCherry-LaM8 complex -

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Basic information

Entry
Database: PDB / ID: 8im0
TitlemCherry-LaM8 complex
Components
  • LaM8
  • MCherry fluorescent protein
KeywordsFLUORESCENT PROTEIN/IMMUNE SYSTEM / PROTEIN BINDING / FLUORESCENT PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
MCherry fluorescent protein
Similarity search - Component
Biological speciesAnaplasma marginale (bacteria)
Camelus bactrianus (Bactrian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsLiang, H. / 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: Int J Mol Sci / Year: 2023
Title: Structural Insights into the Binding of Red Fluorescent Protein mCherry-Specific Nanobodies.
Authors: Liang, H. / Ma, Z. / Wang, Z. / Zhong, P. / Li, R. / Jiang, H. / Zong, X. / Zhong, C. / Liu, X. / Liu, P. / Liu, J. / Zhu, H. / Liu, R. / Ding, Y.
History
DepositionMar 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: MCherry fluorescent protein
B: LaM8


Theoretical massNumber of molelcules
Total (without water)40,6182
Polymers40,6182
Non-polymers00
Water10,575587
1
A: MCherry fluorescent protein

B: LaM8


Theoretical massNumber of molelcules
Total (without water)40,6182
Polymers40,6182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454x-1/2,-y+1/2,-z-11
Buried area1110 Å2
ΔGint-5 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.075, 75.310, 83.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MCherry fluorescent protein


Mass: 26797.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma marginale (bacteria) / Gene: mCherry / Production host: Escherichia coli (E. coli) / References: UniProt: X5DSL3
#2: Antibody LaM8


Mass: 13821.208 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)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl (pH 8.5), 30% (w/v) PEG 4000

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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: Sep 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.31→83.62 Å / Num. obs: 95127 / % possible obs: 98.9 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.019 / Rrim(I) all: 0.065 / Χ2: 0.75 / Net I/σ(I): 18.5 / Num. measured all: 1055879
Reflection shellResolution: 1.31→1.34 Å / % possible obs: 89.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.88 / Num. measured all: 28966 / Num. unique obs: 6239 / CC1/2: 0.621 / Rpim(I) all: 0.43 / Rrim(I) all: 0.988 / Χ2: 0.34 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→50.36 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1896 2000 2.1 %
Rwork0.178 --
obs0.1783 95021 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→50.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 0 587 3231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.117
X-RAY DIFFRACTIONf_dihedral_angle_d8.56376
X-RAY DIFFRACTIONf_chiral_restr0.095380
X-RAY DIFFRACTIONf_plane_restr0.008475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.340.261260.2675877X-RAY DIFFRACTION89
1.34-1.380.24921370.24936345X-RAY DIFFRACTION96
1.38-1.420.21461420.22856615X-RAY DIFFRACTION99
1.42-1.470.21741430.20676674X-RAY DIFFRACTION100
1.47-1.520.21881440.196663X-RAY DIFFRACTION100
1.52-1.580.23071430.18986688X-RAY DIFFRACTION100
1.58-1.650.20331430.18586644X-RAY DIFFRACTION100
1.65-1.740.19811440.18746696X-RAY DIFFRACTION100
1.74-1.850.19441450.18776725X-RAY DIFFRACTION100
1.85-1.990.19681440.17416715X-RAY DIFFRACTION100
1.99-2.190.1941450.16816736X-RAY DIFFRACTION100
2.19-2.510.18991460.17526780X-RAY DIFFRACTION100
2.51-3.160.17931470.17766838X-RAY DIFFRACTION100
3.16-50.360.16531510.15917025X-RAY DIFFRACTION99

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