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- PDB-8dtn: The complex of nanobody 6101 with BCL11A ZF6 -

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Basic information

Entry
Database: PDB / ID: 8dtn
TitleThe complex of nanobody 6101 with BCL11A ZF6
Components
  • B-cell lymphoma/leukemia 11A
  • Nanobody 6101
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 / negative regulation of branching morphogenesis of a nerve / transcription regulatory region nucleic acid binding / negative regulation of dendrite extension / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / negative regulation of dendrite development / regulation of dendrite development / negative regulation of axon extension / positive regulation of collateral sprouting ...negative regulation of neuron remodeling / negative regulation of branching morphogenesis of a nerve / transcription regulatory region nucleic acid binding / negative regulation of dendrite extension / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / negative regulation of dendrite development / regulation of dendrite development / negative regulation of axon extension / positive regulation of collateral sprouting / ALK mutants bind TKIs / cellular response to L-glutamate / paraspeckles / SWI/SNF complex / protein sumoylation / transcription coregulator activity / positive regulation of neuron projection development / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / Signaling by ALK fusions and activated point mutants / negative regulation of neuron projection development / DNA-binding transcription factor binding / postsynapse / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization 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 / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / BCL-11A-like CCHC zinc finger / : / C2H2 zinc finger / 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 ...: / BCL-11A-like CCHC zinc finger / : / C2H2 zinc finger / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BCL11 transcription factor A
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.199 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
Revision 1.1Oct 23, 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: Nanobody 6101
B: B-cell lymphoma/leukemia 11A
C: Nanobody 6101
D: B-cell lymphoma/leukemia 11A
E: Nanobody 6101
F: B-cell lymphoma/leukemia 11A
G: Nanobody 6101
H: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,55016
Polymers66,1928
Non-polymers3598
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-70 kcal/mol
Surface area29330 Å2
MethodPISA
2
A: Nanobody 6101
B: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6384
Polymers16,5482
Non-polymers902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-17 kcal/mol
Surface area7950 Å2
MethodPISA
3
C: Nanobody 6101
D: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6133
Polymers16,5482
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-10 kcal/mol
Surface area7910 Å2
MethodPISA
4
E: Nanobody 6101
F: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6866
Polymers16,5482
Non-polymers1384
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-18 kcal/mol
Surface area8240 Å2
MethodPISA
5
G: Nanobody 6101
H: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6133
Polymers16,5482
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-13 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.933, 54.933, 408.619
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody
Nanobody 6101


Mass: 12726.685 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: 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: 3821.213 Da / Num. of mol.: 4
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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane, pH 6.0-7.0, 0.2 M NaKPO4 and 18%-20% PEG 3350

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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: Mar 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.199→29.28 Å / Num. obs: 37430 / % possible obs: 97.45 % / Redundancy: 7.3 % / Biso Wilson estimate: 35.07 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.05494 / Rpim(I) all: 0.05494 / Rrim(I) all: 0.0777 / Net I/σ(I): 17.13
Reflection shellResolution: 2.199→2.278 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 5.62 / Num. unique obs: 37119 / CC1/2: 0.941 / CC star: 0.985 / Rpim(I) all: 0.128 / Rrim(I) all: 0.181 / % possible all: 93.61

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Processing

Software
NameVersionClassification
BIOMOLdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
iMOSFLM7.2.2data reduction
PHENIX1.13-2998-000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.199→29.279 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1985 5.35 %
Rwork0.1949 35134 -
obs0.1969 37119 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.95 Å2 / Biso mean: 35.7174 Å2 / Biso min: 13.48 Å2
Refinement stepCycle: final / Resolution: 2.199→29.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4511 0 8 401 4920
Biso mean--37.58 39.91 -
Num. residues----583
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1991-2.25410.26831320.2063225693
2.2541-2.3150.29981390.2179242496
2.315-2.38310.32281430.2121249497
2.3831-2.460.26461330.2145239998
2.46-2.54790.24471360.2128246697
2.5479-2.64980.27931370.2183247897
2.6498-2.77030.27941380.2156246698
2.7703-2.91620.27921400.2407251598
2.9162-3.09880.27861400.2313248397
3.0988-3.33770.24131380.214249597
3.3377-3.6730.22211460.1974259198
3.673-4.20320.2021480.1655257799
4.2032-5.29050.17681510.14552660100
5.2905-29.2780.21141640.1972830100

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