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- PDB-6rpj: A Non-blocking anti-CTLA-4 Nanobody complexed with CTLA-4 -

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Basic information

Entry
Database: PDB / ID: 6rpj
TitleA Non-blocking anti-CTLA-4 Nanobody complexed with CTLA-4
Components
  • A non-blocking CTLA-4 nanobody
  • Cytotoxic T-lymphocyte protein 4Cytotoxic T cell
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 speciesHomo sapiens (human)
Camelus bactrianus (Bactrian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsGao, H. / Zhou, A. / Zhang, F.
CitationJournal: To Be Published
Title: A Non-blocking anti-CTLA-4 Nanobody complexed with CTLA-4
Authors: Gao, H. / Zhou, A.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / refine / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Nov 11, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _atom_site.auth_seq_id / _chem_comp.pdbx_synonyms ..._atom_site.auth_seq_id / _chem_comp.pdbx_synonyms / _pdbx_nonpoly_scheme.pdb_seq_num / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytotoxic T-lymphocyte protein 4
B: A non-blocking CTLA-4 nanobody
C: Cytotoxic T-lymphocyte protein 4
D: A non-blocking CTLA-4 nanobody
E: Cytotoxic T-lymphocyte protein 4
F: A non-blocking CTLA-4 nanobody
G: Cytotoxic T-lymphocyte protein 4
H: A non-blocking CTLA-4 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,42217
Polymers116,3898
Non-polymers2,0339
Water362
1
G: Cytotoxic T-lymphocyte protein 4
H: A non-blocking CTLA-4 nanobody
hetero molecules

A: Cytotoxic T-lymphocyte protein 4
B: A non-blocking CTLA-4 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1748
Polymers58,1954
Non-polymers9794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_544x,y-1,z-11
Buried area6430 Å2
ΔGint-13 kcal/mol
Surface area21620 Å2
MethodPISA
2
C: Cytotoxic T-lymphocyte protein 4
D: A non-blocking CTLA-4 nanobody
E: Cytotoxic T-lymphocyte protein 4
F: A non-blocking CTLA-4 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2499
Polymers58,1954
Non-polymers1,0545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-12 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)309.977, 75.708, 83.047
Angle α, β, γ (deg.)90.00, 100.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Antibody , 2 types, 8 molecules ACEGBDFH

#1: Protein
Cytotoxic T-lymphocyte protein 4 / Cytotoxic T cell / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4


Mass: 13893.714 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4, CD152 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P16410
#2: Antibody
A non-blocking CTLA-4 nanobody


Mass: 15203.618 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Sugars , 2 types, 7 molecules

#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3 / Source method: isolated from a natural source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 4.61 Å3/Da / Density % sol: 73.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 R 300K / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 30159 / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 8
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 3 / Num. unique obs: 1926 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→47.57 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.873 / SU B: 51.975 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26155 1455 5 %RANDOM
Rwork0.24889 ---
obs0.2495 27487 95.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.735 Å2
Baniso -1Baniso -2Baniso -3
1--3.74 Å20 Å2-3.42 Å2
2--1.28 Å20 Å2
3---3.46 Å2
Refinement stepCycle: LAST / Resolution: 3.25→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7271 0 130 2 7403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0137594
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176729
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.67310350
X-RAY DIFFRACTIONr_angle_other_deg1.051.59215645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.7115.3341002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.68722.406345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.364151147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1121544
X-RAY DIFFRACTIONr_chiral_restr0.0280.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021569
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_it1.1196.2033898
X-RAY DIFFRACTIONr_mcbond_other1.1196.2023897
X-RAY DIFFRACTIONr_mcangle_it2.1389.2924862
X-RAY DIFFRACTIONr_mcangle_other2.1379.2934863
X-RAY DIFFRACTIONr_scbond_it0.6966.2873694
X-RAY DIFFRACTIONr_scbond_other0.6966.2873694
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4319.4145480
X-RAY DIFFRACTIONr_long_range_B_refined3.42268.4677370
X-RAY DIFFRACTIONr_long_range_B_other3.42168.4837371
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.245→3.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 88 -
Rwork0.347 1926 -
obs--89.39 %
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)
14.6752.75333.16771.93672.09552.45991.07750.4893-1.14580.2883-0.0966-0.61770.41040.1471-0.98090.69960.4891-0.2220.52-0.31310.642516.78232.409783.2668
26.8919-0.58751.16960.91190.22261.45640.1254-0.07150.4046-0.04070.0723-0.02690.0579-0.048-0.19770.32890.00150.03630.3039-0.10420.3135-3.189150.39988.9171
36.1346-0.615-0.62830.4303-0.05391.82150.1283-0.60541.01510.0259-0.1434-0.0791-0.0249-0.11970.01520.27420.0464-0.00570.3481-0.33170.493422.464526.548250.1094
46.67850.52160.84980.52810.69541.7937-0.01940.0437-0.2492-0.03450.2381-0.11250.0864-0.0688-0.21870.32450.01820.0360.3206-0.0740.3055.81048.422238.0756
53.674-0.74620.69352.58250.05860.89340.06550.4873-0.0305-0.0222-0.0070.10230.04360.0342-0.05850.33040.04110.05490.3122-0.17760.291235.849.265631.1961
65.6784-0.0951.79290.0888-0.31863.0414-0.1398-0.60520.1407-0.091-0.091-0.06640.15890.01350.23080.30030.05020.01640.4067-0.11120.308450.935812.171253.8215
75.03910.73841.31852.8502-0.31050.69850.215-0.55740.1043-0.0686-0.03540.08130.0082-0.157-0.17960.32160.02360.06240.3438-0.17890.256136.9676-26.271823.999
86.30120.53640.04840.28920.11341.93180.08220.7766-0.12530.14650.05020.13690.01850.5179-0.13240.29360.12440.04090.5742-0.19640.153459.2419-28.71368.2131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 120
2X-RAY DIFFRACTION2B1 - 125
3X-RAY DIFFRACTION3C3 - 120
4X-RAY DIFFRACTION4D1 - 125
5X-RAY DIFFRACTION5E3 - 121
6X-RAY DIFFRACTION6F1 - 125
7X-RAY DIFFRACTION7G3 - 120
8X-RAY DIFFRACTION8H1 - 125

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