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- PDB-3p11: anti-EGFR/HER3 Fab DL11 in complex with domains I-III of the HER3... -

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Basic information

Entry
Database: PDB / ID: 3p11
Titleanti-EGFR/HER3 Fab DL11 in complex with domains I-III of the HER3 extracellular region
Components
  • Fab DL11 heavy chain
  • Fab DL11 light chain
  • Receptor tyrosine-protein kinase erbB-3
KeywordsIMMUNE SYSTEM / beta-sandwich / antigens HER3
Function / homology
Function and homology information


neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade ...neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade / peripheral nervous system development / negative regulation of cell adhesion / ErbB-3 class receptor binding / negative regulation of motor neuron apoptotic process / motor neuron apoptotic process / growth factor binding / ERBB2 Activates PTK6 Signaling / ERBB2-ERBB3 signaling pathway / ERBB2 Regulates Cell Motility / protein tyrosine kinase activator activity / Signaling by ERBB4 / PI3K events in ERBB2 signaling / lateral plasma membrane / negative regulation of signal transduction / Schwann cell development / Signaling by ERBB2 / extrinsic apoptotic signaling pathway in absence of ligand / myelination / Downregulation of ERBB2:ERBB3 signaling / SHC1 events in ERBB2 signaling / cell surface receptor protein tyrosine kinase signaling pathway / basal plasma membrane / positive regulation of epithelial cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / Signaling by ERBB2 TMD/JMD mutants / receptor protein-tyrosine kinase / Signaling by ERBB2 KD Mutants / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / regulation of cell population proliferation / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / neuron apoptotic process / basolateral plasma membrane / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein kinase activity / positive regulation of MAPK cascade / apical plasma membrane / protein heterodimerization activity / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process / signal transduction / extracellular space / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Alpha-Beta Horseshoe / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain ...Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Alpha-Beta Horseshoe / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / 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 / : / Ribbon / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsEigenbrot, C. / Shia, S.
CitationJournal: Cancer Cell / Year: 2011
Title: A two-in-one antibody against HER3 and EGFR has superior inhibitory activity compared with monospecific antibodies.
Authors: Schaefer, G. / Haber, L. / Crocker, L.M. / Shia, S. / Shao, L. / Dowbenko, D. / Totpal, K. / Wong, A. / Lee, C.V. / Stawicki, S. / Clark, R. / Fields, C. / Lewis Phillips, G.D. / Prell, R.A. ...Authors: Schaefer, G. / Haber, L. / Crocker, L.M. / Shia, S. / Shao, L. / Dowbenko, D. / Totpal, K. / Wong, A. / Lee, C.V. / Stawicki, S. / Clark, R. / Fields, C. / Lewis Phillips, G.D. / Prell, R.A. / Danilenko, D.M. / Franke, Y. / Stephan, J.P. / Hwang, J. / Wu, Y. / Bostrom, J. / Sliwkowski, M.X. / Fuh, G. / Eigenbrot, C.
History
DepositionSep 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab DL11 heavy chain
L: Fab DL11 light chain
A: Receptor tyrosine-protein kinase erbB-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1336
Polymers105,2663
Non-polymers8673
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.392, 48.397, 130.381
Angle α, β, γ (deg.)90.00, 127.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Fab DL11 heavy chain


Mass: 24000.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pW0579-3 / Production host: Escherichia coli (E. coli)
#2: Antibody Fab DL11 light chain


Mass: 23385.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pW0579-3 / Production host: Escherichia coli (E. coli)
#3: Protein Receptor tyrosine-protein kinase erbB-3 / Proto-oncogene-like protein c-ErbB-3 / Tyrosine kinase-type cell surface receptor HER3


Mass: 57879.645 Da / Num. of mol.: 1 / Fragment: domains I-III, UNP residues 20-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB3, HER3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P21860, receptor protein-tyrosine kinase
#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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 2
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
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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: PEG 1500, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2009 / Details: Si
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 13436 / Num. obs: 13436 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.5 % / Rsym value: 0.11 / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.862 / SU B: 136.102 / SU ML: 0.889 / Cross valid method: THROUGHOUT / ESU R Free: 0.995 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32299 574 5.1 %RANDOM
Rwork0.24542 ---
obs0.24922 10774 99.92 %-
all-13378 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 159.543 Å2
Baniso -1Baniso -2Baniso -3
1--7.11 Å2-0 Å2-4.81 Å2
2--2.85 Å2-0 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 3.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7149 0 56 0 7205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227394
X-RAY DIFFRACTIONr_bond_other_d0.0010.024957
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.96110064
X-RAY DIFFRACTIONr_angle_other_deg0.816312092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54424.153313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.147151177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3661541
X-RAY DIFFRACTIONr_chiral_restr0.0580.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218251
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021454
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_refined0.1520.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.46514644
X-RAY DIFFRACTIONr_mcbond_other0.04711894
X-RAY DIFFRACTIONr_mcangle_it1.08837504
X-RAY DIFFRACTIONr_scbond_it1.78232750
X-RAY DIFFRACTIONr_scangle_it3.15452560
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.7→3.899 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.405 95 -
Rwork0.345 1517 -
obs--100 %
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)
12.2195-1.26792.09056.3613-0.43957.4268-0.0161-0.0188-0.0975-0.13370.02760.27190.15980.5046-0.01150.0793-0.0220.09920.0746-0.05380.165133.470832.8494-9.0325
24.7858-1.8780.8875.32191.13144.18450.2624-0.8561-0.20250.0147-0.0749-0.2144-0.23030.6103-0.18740.1652-0.01980.02210.53620.08330.038943.665629.942523.1522
36.4936-0.59851.12395.55021.30453.530.16570.1047-0.874-0.0471-0.14390.45330.209-0.3294-0.02180.1571-0.17260.01140.68560.11280.3039-14.3159-8.599-86.2934
45.39296.2644-2.52827.3001-2.95161.2004-0.67280.641.3305-1.29980.96631.48090.5788-0.3656-0.29351.91660.17890.20141.84740.05431.1446-27.565416.431-95.3811
55.0472-0.3602-7.347222.837-0.89418.30720.2935-0.01540.80310.33420.03561.32010.0316-0.2352-0.32920.45690.1446-0.0690.82280.06510.4555-26.344213.241-84.5845
624.819321.86771.405429.4462.15740.1632-0.0588-2.79771.1016-1.2214-0.04380.2291-0.11290.05920.10260.6054-0.0062-0.02361.1475-0.06360.5108-20.379114.2688-77.1534
710.32611.99414.40260.91080.00793.30670.3886-0.95772.04150.9359-0.56220.6911-1.1503-0.39490.17361.48-0.15380.35571.4576-0.0491.3025-20.561322.8784-63.3953
830.87844.3442-17.573542.2115-13.040612.6943-1.4558-2.2993-0.32211.66181.58011.0470.41440.7688-0.12431.2162-0.1108-0.37860.6257-0.1530.6649-9.57119.5911-62.7529
93.5789-8.6108-3.396721.04239.17926.4188-0.5939-0.2616-0.39471.20680.37290.9523-0.1453-0.2690.2210.7021-0.174-0.25331.0974-0.38450.954-5.573616.3477-56.4016
104.8626-0.32080.75998.24370.11426.9601-0.2240.1361-0.3162-0.38510.32660.1520.2421-0.2721-0.10260.1702-0.18170.04130.2293-0.06750.054520.107225.9959-39.4263
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 123
2X-RAY DIFFRACTION1L1 - 107
3X-RAY DIFFRACTION2H124 - 230
4X-RAY DIFFRACTION2L108 - 230
5X-RAY DIFFRACTION3A1 - 190
6X-RAY DIFFRACTION4A191 - 207
7X-RAY DIFFRACTION5A208 - 225
8X-RAY DIFFRACTION6A226 - 238
9X-RAY DIFFRACTION7A239 - 269
10X-RAY DIFFRACTION8A270 - 284
11X-RAY DIFFRACTION9A285 - 303
12X-RAY DIFFRACTION10A304 - 513

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