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- PDB-6azk: Structure of cetuximab with aminoheptanoic acid-linked N-(3-hydro... -

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Basic information

Entry
Database: PDB / ID: 6azk
TitleStructure of cetuximab with aminoheptanoic acid-linked N-(3-hydroxypropyl)-L-arginine meditope variant
Components
  • cetuximab Fab heavy chain
  • cetuximab Fab light chain
  • meditope
KeywordsIMMUNE SYSTEM / antibody / anti-EGFR
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / IgG H chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.477 Å
AuthorsBzymek, K.P. / Williams, J.C.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Meditope-Fab interaction: threading the hole.
Authors: Bzymek, K.P. / Ma, Y. / Avery, K.N. / Horne, D.A. / Williams, J.C.
History
DepositionSep 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cetuximab Fab light chain
B: cetuximab Fab heavy chain
C: cetuximab Fab light chain
D: cetuximab Fab heavy chain
E: meditope
F: meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1208
Polymers96,9286
Non-polymers1922
Water9,476526
1
A: cetuximab Fab light chain
B: cetuximab Fab heavy chain
E: meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5604
Polymers48,4643
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-46 kcal/mol
Surface area18440 Å2
MethodPISA
2
C: cetuximab Fab light chain
D: cetuximab Fab heavy chain
F: meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5604
Polymers48,4643
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-38 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.360, 82.930, 212.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody cetuximab Fab light chain


Mass: 23287.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chimeric murine/human antibody purified from Erbitux
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: unidentified (others) / References: UniProt: P01834
#2: Antibody cetuximab Fab heavy chain


Mass: 23725.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chimeric murine/human antibody purified from Erbitux
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: unidentified (others) / References: UniProt: S6B291
#3: Protein/peptide meditope


Mass: 1450.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence of cetuximab Fab light chain in this entry matches to the sequence of cetuximab Fab light ...Sequence of cetuximab Fab light chain in this entry matches to the sequence of cetuximab Fab light chain from the first deposited cetuximab structure in PDB (1yy8)

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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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citrate pH 5, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.477→33.113 Å / Num. obs: 40781 / % possible obs: 98.8 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.8
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 2690 / CC1/2: 0.954 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gw1

4gw1


Resolution: 2.477→33.113 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 19.04
RfactorNum. reflection% reflection
Rfree0.2131 2039 5 %
Rwork0.1701 --
obs0.1723 40779 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.477→33.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6769 0 10 526 7305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056978
X-RAY DIFFRACTIONf_angle_d1.0779511
X-RAY DIFFRACTIONf_dihedral_angle_d11.0954174
X-RAY DIFFRACTIONf_chiral_restr0.071071
X-RAY DIFFRACTIONf_plane_restr0.0041216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4773-2.53490.2561180.20972242X-RAY DIFFRACTION89
2.5349-2.59830.27261350.18652570X-RAY DIFFRACTION99
2.5983-2.66850.24411350.17442562X-RAY DIFFRACTION99
2.6685-2.7470.22921330.18042544X-RAY DIFFRACTION99
2.747-2.83560.23551370.18642587X-RAY DIFFRACTION99
2.8356-2.93690.2661340.18722560X-RAY DIFFRACTION100
2.9369-3.05440.23681360.18642573X-RAY DIFFRACTION100
3.0544-3.19330.25221360.18782592X-RAY DIFFRACTION100
3.1933-3.36150.23971360.17222575X-RAY DIFFRACTION100
3.3615-3.57190.18671370.16182603X-RAY DIFFRACTION100
3.5719-3.84730.18111370.16072600X-RAY DIFFRACTION100
3.8473-4.23380.1851380.1412632X-RAY DIFFRACTION100
4.2338-4.84480.15831390.12572630X-RAY DIFFRACTION100
4.8448-6.09770.20081400.16432673X-RAY DIFFRACTION100
6.0977-33.11640.22141480.21392797X-RAY DIFFRACTION99

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