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- PDB-6b3s: Crystal structure of the Fab fragment of necitumumab (Fab11F8) in... -

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Basic information

Entry
Database: PDB / ID: 6b3s
TitleCrystal structure of the Fab fragment of necitumumab (Fab11F8) in complex with domain III from a cetuximab resistant variant of EGFR (sEGFRd3-S468R)
Components
  • (Necitumumab Fab ...) x 2
  • Epidermal growth factor receptor
KeywordsTRANSFERASE/immune system / Therapeutic antibody / Cetuximab resistance / Somatic mutation / Colorectal cancer / TRANSFERASE / TRANSFERASE-immune system complex
Function / homology
Function and homology information


response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity ...response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / response to UV-A / epidermal growth factor binding / PLCG1 events in ERBB2 signaling / tongue development / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Signaling by EGFR / response to cobalamin / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / eyelid development in camera-type eye / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / embryonic placenta development / positive regulation of bone resorption / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / positive regulation of phosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / cellular response to cadmium ion / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of DNA repair / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / neurogenesis / cellular response to dexamethasone stimulus / ossification / positive regulation of synaptic transmission, glutamatergic / regulation of ERK1 and ERK2 cascade / neuron projection morphogenesis / basal plasma membrane / positive regulation of epithelial cell proliferation / positive regulation of superoxide anion generation / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / cellular response to estradiol stimulus / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / liver regeneration / positive regulation of protein localization to plasma membrane / EGFR downregulation / positive regulation of smooth muscle cell proliferation / cellular response to amino acid stimulus / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / lung development / clathrin-coated endocytic vesicle membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / negative regulation of protein catabolic process / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / kinase binding / cell-cell adhesion / ruffle membrane / positive regulation of miRNA transcription
Similarity search - Function
24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Receptor L-domain / Furin-like cysteine-rich domain ...24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Epidermal growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFerguson, K.M. / Bagchi, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA112552 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008275 United States
CitationJournal: Mol. Cancer Ther. / Year: 2018
Title: Molecular Basis for Necitumumab Inhibition of EGFR Variants Associated with Acquired Cetuximab Resistance.
Authors: Bagchi, A. / Haidar, J.N. / Eastman, S.W. / Vieth, M. / Topper, M. / Iacolina, M.D. / Walker, J.M. / Forest, A. / Shen, Y. / Novosiadly, R.D. / Ferguson, K.M.
History
DepositionSep 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / 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 / 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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epidermal growth factor receptor
H: Necitumumab Fab Heavy chain
L: Necitumumab Fab Light chain
B: Epidermal growth factor receptor
C: Necitumumab Fab Heavy chain
D: Necitumumab Fab Light chain
E: Epidermal growth factor receptor
F: Necitumumab Fab Heavy chain
G: Necitumumab Fab Light chain
I: Epidermal growth factor receptor
J: Necitumumab Fab Heavy chain
K: Necitumumab Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,58327
Polymers281,82812
Non-polymers5,75415
Water1,24369
1
A: Epidermal growth factor receptor
H: Necitumumab Fab Heavy chain
L: Necitumumab Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9107
Polymers70,4573
Non-polymers1,4534
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epidermal growth factor receptor
C: Necitumumab Fab Heavy chain
D: Necitumumab Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0737
Polymers70,4573
Non-polymers1,6154
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Epidermal growth factor receptor
F: Necitumumab Fab Heavy chain
G: Necitumumab Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0737
Polymers70,4573
Non-polymers1,6154
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: Epidermal growth factor receptor
J: Necitumumab Fab Heavy chain
K: Necitumumab Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5276
Polymers70,4573
Non-polymers1,0703
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.943, 80.756, 172.901
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number3
Space group name H-MP121

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Components

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Antibody , 2 types, 8 molecules HCFJLDGK

#2: Antibody
Necitumumab Fab Heavy chain


Mass: 23547.330 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): NS0 / Production host: Mus musculus (house mouse)
#3: Antibody
Necitumumab Fab Light chain


Mass: 23053.557 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): NS0 / Production host: Mus musculus (house mouse)

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Protein / Non-polymers , 2 types, 73 molecules ABEI

#1: Protein
Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


Mass: 23856.203 Da / Num. of mol.: 4 / Mutation: S468R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, HER1 / Plasmid: pfastbac / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00533, receptor protein-tyrosine kinase
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 15 molecules

#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 67.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM sodium acetate, 200 mM potassium citrate, 15-20% PEG3350
PH range: 6.0-6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.795→50 Å / Num. obs: 100220 / % possible obs: 97 % / Redundancy: 4.2 % / Biso Wilson estimate: 63.32 Å2 / Rmerge(I) obs: 0.162 / Net I/σ(I): 6
Reflection shellResolution: 2.8→2.93 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.703 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B2U

3b2u


Resolution: 2.8→47 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.91
RfactorNum. reflection% reflection
Rfree0.245 4974 4.97 %
Rwork0.208 --
obs0.209 100134 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 73.81 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18519 0 377 69 18965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319378
X-RAY DIFFRACTIONf_angle_d0.65826495
X-RAY DIFFRACTIONf_dihedral_angle_d8.22611480
X-RAY DIFFRACTIONf_chiral_restr0.0533125
X-RAY DIFFRACTIONf_plane_restr0.0033353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7945-2.82630.39771200.30852065X-RAY DIFFRACTION64
2.8263-2.85950.4231620.34083081X-RAY DIFFRACTION93
2.8595-2.89440.40581670.31383144X-RAY DIFFRACTION96
2.8944-2.9310.34761820.30583167X-RAY DIFFRACTION97
2.931-2.96960.36081710.28483191X-RAY DIFFRACTION97
2.9696-3.01030.30791660.27073201X-RAY DIFFRACTION98
3.0103-3.05330.36471800.26383204X-RAY DIFFRACTION98
3.0533-3.09880.34811830.27013200X-RAY DIFFRACTION98
3.0988-3.14730.35391930.26173156X-RAY DIFFRACTION98
3.1473-3.19880.30121580.27213229X-RAY DIFFRACTION97
3.1988-3.2540.28191690.24923149X-RAY DIFFRACTION97
3.254-3.31310.31471670.2363218X-RAY DIFFRACTION98
3.3131-3.37680.26811630.22753288X-RAY DIFFRACTION98
3.3768-3.44580.28171320.22623188X-RAY DIFFRACTION98
3.4458-3.52070.27411470.22413260X-RAY DIFFRACTION98
3.5207-3.60250.26051740.22083199X-RAY DIFFRACTION98
3.6025-3.69260.26351530.22023253X-RAY DIFFRACTION98
3.6926-3.79240.25141600.21563191X-RAY DIFFRACTION98
3.7924-3.90390.25391550.20723258X-RAY DIFFRACTION97
3.9039-4.02990.21811550.19553255X-RAY DIFFRACTION97
4.0299-4.17380.21091740.18443158X-RAY DIFFRACTION97
4.1738-4.34080.2251620.17013237X-RAY DIFFRACTION98
4.3408-4.53820.1891810.16053252X-RAY DIFFRACTION98
4.5382-4.77730.17752010.15343205X-RAY DIFFRACTION98
4.7773-5.07620.19191870.14853222X-RAY DIFFRACTION97
5.0762-5.46760.18391620.15753235X-RAY DIFFRACTION97
5.4676-6.01690.21941550.18473221X-RAY DIFFRACTION96
6.0169-6.88520.21691750.1973232X-RAY DIFFRACTION96
6.8852-8.66570.23341460.2173280X-RAY DIFFRACTION96
8.6657-47.00990.23571740.22093221X-RAY DIFFRACTION93

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