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- PDB-8dtu: The complex of nanobody 5344N74D with BCL11A ZF6. -

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Basic information

Entry
Database: PDB / ID: 8dtu
TitleThe complex of nanobody 5344N74D with BCL11A ZF6.
Components
  • (Nanobody 5344N74D) x 2
  • B-cell lymphoma/leukemia 11A
KeywordsDNA BINDING PROTEIN / Nanobody / BCL11A / Transcription factor / Zinc finger domain / protein degradation / gamma globin / sickle cells
Function / homology
Function and homology information


negative regulation of neuron remodeling / transcription regulatory region nucleic acid binding / negative regulation of branching morphogenesis of a nerve / negative regulation of dendrite extension / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / regulation of dendrite development / negative regulation of dendrite development / negative regulation of axon extension / cellular response to L-glutamate ...negative regulation of neuron remodeling / transcription regulatory region nucleic acid binding / negative regulation of branching morphogenesis of a nerve / negative regulation of dendrite extension / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / regulation of dendrite development / negative regulation of dendrite development / negative regulation of axon extension / cellular response to L-glutamate / positive regulation of collateral sprouting / paraspeckles / ALK mutants bind TKIs / SWI/SNF complex / protein sumoylation / transcription coregulator activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / positive regulation of neuron projection development / Signaling by ALK fusions and activated point mutants / negative regulation of neuron projection development / postsynapse / DNA-binding transcription factor binding / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
B-cell lymphoma/leukemia 11A
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.447 Å
AuthorsYin, M. / Tenglin, K. / Zhai, L. / Dassama, L.M. / Orkin, S.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Evolution of nanobodies specific for BCL11A.
Authors: Yin, M. / Izadi, M. / Tenglin, K. / Viennet, T. / Zhai, L. / Zheng, G. / Arthanari, H. / Dassama, L.M.K. / Orkin, S.H.
History
DepositionJul 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Nanobody 5344N74D
A: Nanobody 5344N74D
C: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4164
Polymers16,3513
Non-polymers651
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-15 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.507, 57.507, 157.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody Nanobody 5344N74D


Mass: 714.872 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Antibody Nanobody 5344N74D


Mass: 12152.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide B-cell lymphoma/leukemia 11A / BCL-11A / B-cell CLL/lymphoma 11A / COUP-TF-interacting protein 1 / Ecotropic viral integration ...BCL-11A / B-cell CLL/lymphoma 11A / COUP-TF-interacting protein 1 / Ecotropic viral integration site 9 protein homolog / EVI-9 / Zinc finger protein 856 / ZF6


Mass: 3483.155 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL11A, CTIP1, EVI9, KIAA1809, ZNF856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H165
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 7.5-8.2, 2.2M Li2SO4. / PH range: 7.5-8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.447→40.664 Å / Num. obs: 10390 / % possible obs: 96.56 % / Redundancy: 35 % / Biso Wilson estimate: 54.57 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1547 / Rpim(I) all: 0.02625 / Rrim(I) all: 0.157 / Net I/σ(I): 24.49
Reflection shellResolution: 2.447→2.535 Å / Redundancy: 36.2 % / Rmerge(I) obs: 2.123 / Mean I/σ(I) obs: 2.77 / Num. unique obs: 1011 / CC1/2: 0.938 / CC star: 0.984 / Rpim(I) all: 0.3513 / Rrim(I) all: 2.152 / % possible all: 90.83

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.447→40.66 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 34.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 1011 10.07 %
Rwork0.2613 --
obs0.2639 10390 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.447→40.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 1 17 1154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121159
X-RAY DIFFRACTIONf_angle_d1.3181563
X-RAY DIFFRACTIONf_dihedral_angle_d23.302417
X-RAY DIFFRACTIONf_chiral_restr0.057167
X-RAY DIFFRACTIONf_plane_restr0.005197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4471-2.57610.37581400.38251168X-RAY DIFFRACTION91
2.5761-2.73750.42251290.36821218X-RAY DIFFRACTION93
2.7375-2.94880.36371380.33691226X-RAY DIFFRACTION96
2.9488-3.24540.36071430.31721304X-RAY DIFFRACTION98
3.2454-3.71470.28531470.26921315X-RAY DIFFRACTION99
3.7147-4.67910.21921500.22161346X-RAY DIFFRACTION100
4.6791-40.660.27821640.22851456X-RAY DIFFRACTION100

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