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- PDB-6rqm: A blocking anti-CTLA-4 Nanobody (KN044) complexed with CTLA-4 -

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Basic information

Entry
Database: PDB / ID: 6rqm
TitleA blocking anti-CTLA-4 Nanobody (KN044) complexed with CTLA-4
Components
  • A blocking anti-CTLA-4 nanobody (KN044)
  • Cytotoxic T-lymphocyte protein 4
KeywordsIMMUNE SYSTEM / Antibody / check-point / CTLA-4 / receptor
Function / homology
Function and homology information


protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response ...protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response / immune response / positive regulation of apoptotic process / external side of plasma membrane / DNA damage response / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane
Similarity search - Function
Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cytotoxic T-lymphocyte protein 4
Similarity search - Component
Biological speciesCamelus bactrianus (Bactrian camel)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhang, F. / Zhou, A. / Gao, H.
CitationJournal: To Be Published
Title: A blocking anti-CTLA-4 Nanobody (KN044) complexed with CTLA-4
Authors: Gao, H. / Zhou, A.
History
DepositionMay 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: A blocking anti-CTLA-4 nanobody (KN044)
A: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)28,6902
Polymers28,6902
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-8 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.770, 98.770, 110.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody A blocking anti-CTLA-4 nanobody (KN044)


Mass: 15308.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag residues are missing due to weak electron density.
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Protein Cytotoxic T-lymphocyte protein 4 / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4


Mass: 13381.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: missing residues due to weak electron density / Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4, CD152 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P16410
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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3→68 Å / Num. obs: 6820 / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.032 / Rrim(I) all: 0.121 / Χ2: 1.03 / Net I/σ(I): 18.8
Reflection shellResolution: 3→3.18 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 3 / Num. unique obs: 1068 / Χ2: 0.99 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JDS, 3OSK

5jds

3osk


Resolution: 3→67.73 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.887 / SU B: 62.596 / SU ML: 0.469 / Cross valid method: THROUGHOUT / ESU R Free: 0.501 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31258 340 5 %RANDOM
Rwork0.24972 ---
obs0.25272 6452 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 93.615 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å21.02 Å20 Å2
2--2.03 Å2-0 Å2
3----6.59 Å2
Refinement stepCycle: LAST / Resolution: 3→67.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 0 0 1781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0131821
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171637
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.642480
X-RAY DIFFRACTIONr_angle_other_deg1.0781.5663794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79422.65879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67815273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.884158
X-RAY DIFFRACTIONr_chiral_restr0.0320.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4797.853953
X-RAY DIFFRACTIONr_mcbond_other1.487.851952
X-RAY DIFFRACTIONr_mcangle_it2.68111.7721186
X-RAY DIFFRACTIONr_mcangle_other2.6811.7741187
X-RAY DIFFRACTIONr_scbond_it1.1857.894867
X-RAY DIFFRACTIONr_scbond_other1.1847.897868
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.20411.7741295
X-RAY DIFFRACTIONr_long_range_B_refined4.29988.0791858
X-RAY DIFFRACTIONr_long_range_B_other4.29888.1131859
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 25 -
Rwork0.39 451 -
obs--99.79 %
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)
14.2611.03460.68920.5576-0.02981.54930.2995-0.59450.04970.0192-0.3898-0.14710.076-0.54660.09040.1560.0121-0.00590.54020.11740.095546.7511-5.0346-11.1111
23.28570.20840.66190.67611.19412.41770.09230.1192-0.184-0.0107-0.1347-0.0474-0.12450.01110.04240.2076-0.0259-0.06910.2440.11610.086372.7993-8.0061-19.9516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 128
2X-RAY DIFFRACTION2A4 - 119

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