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Basic information

Entry
Database: PDB / ID: 4tuo
TitleCrystal structure of monoclonal antibody against neuroblastoma associated antigen.
Components
  • Heavy chain of monoclonal antibody against neuroblastoma associated antigen
  • Light chain of monoclonal antibody against neuroblastoma associated antigen
KeywordsIMMUNE SYSTEM / Neuroblastoma
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGolik, P. / Grudnik, P. / Horwacik, I. / Zdzalik, M. / Rokita, H. / Dubin, G.
CitationJournal: Mol.Cell Proteomics / Year: 2015
Title: Structural Basis of GD2 Ganglioside and Mimetic Peptide Recognition by 14G2a Antibody.
Authors: Horwacik, I. / Golik, P. / Grudnik, P. / Kolinski, M. / Zdzalik, M. / Rokita, H. / Dubin, G.
History
DepositionJun 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 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
A: Heavy chain of monoclonal antibody against neuroblastoma associated antigen
B: Light chain of monoclonal antibody against neuroblastoma associated antigen
C: Heavy chain of monoclonal antibody against neuroblastoma associated antigen
D: Light chain of monoclonal antibody against neuroblastoma associated antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3038
Polymers94,0014
Non-polymers2,3024
Water12,394688
1
A: Heavy chain of monoclonal antibody against neuroblastoma associated antigen
B: Light chain of monoclonal antibody against neuroblastoma associated antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1514
Polymers47,0002
Non-polymers1,1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-17 kcal/mol
Surface area18720 Å2
MethodPISA
2
C: Heavy chain of monoclonal antibody against neuroblastoma associated antigen
D: Light chain of monoclonal antibody against neuroblastoma associated antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1514
Polymers47,0002
Non-polymers1,1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-14 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.087, 61.089, 65.358
Angle α, β, γ (deg.)107.79, 113.43, 95.68
Int Tables number1
Space group name H-MP1

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody Heavy chain of monoclonal antibody against neuroblastoma associated antigen


Mass: 22748.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Light chain of monoclonal antibody against neuroblastoma associated antigen


Mass: 24251.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Sugars , 2 types, 2 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-[2-acetamido-2-deoxy-beta- ...N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-[2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1127.999 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-8DNeup5Aca2-3[DGalpNAcb1-4]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-3-4/a4-b1_b3-c2_b4-e1_c8-d2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{}}[(4+1)][b-D-GalpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-[2-acetamido-2-deoxy-beta- ...N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-[2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)]beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1127.999 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-8DNeup5Aca2-3[DGalpNAcb1-4]DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-3-4/a4-b1_b3-c2_b4-e1_c8-d2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{}}[(4+1)][b-D-GalpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 690 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Bis-tris, PEG 3350, NaCl / PH range: 6.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.88563 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88563 Å / Relative weight: 1
ReflectionResolution: 1.55→56.28 Å / Num. obs: 99734 / % possible obs: 90.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 11
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.7 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F8T

1f8t


Resolution: 1.55→56.28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.699 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20637 4981 5 %RANDOM
Rwork0.16627 ---
obs0.16826 94753 90.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.163 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20.04 Å2-0.17 Å2
2--1 Å2-0.26 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.55→56.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6396 0 156 688 7240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.026835
X-RAY DIFFRACTIONr_bond_other_d0.0010.026121
X-RAY DIFFRACTIONr_angle_refined_deg2.0611.9789376
X-RAY DIFFRACTIONr_angle_other_deg0.922314236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0775890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6824.198243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.306151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9411523
X-RAY DIFFRACTIONr_chiral_restr0.1250.21103
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021487
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_it1.5621.5223458
X-RAY DIFFRACTIONr_mcbond_other1.5611.5213457
X-RAY DIFFRACTIONr_mcangle_it2.3122.2814323
X-RAY DIFFRACTIONr_mcangle_other2.3122.2814324
X-RAY DIFFRACTIONr_scbond_it2.2051.6633377
X-RAY DIFFRACTIONr_scbond_other2.2051.6643378
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2182.425031
X-RAY DIFFRACTIONr_long_range_B_refined4.6113.1827793
X-RAY DIFFRACTIONr_long_range_B_other4.50912.7797470
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 376 -
Rwork0.225 6746 -
obs--87.34 %

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