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Basic information

Entry
Database: PDB / ID: 3be1
TitleDual specific bH1 Fab in complex with the extracellular domain of HER2/ErbB-2
Components
  • Fab Fragment-Heavy Chain
  • Fab Fragment-Light Chain
  • Receptor tyrosine-protein kinase erbB-2
KeywordsTRANSFERASE / Fab Complex / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphorylation / Receptor / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / semaphorin receptor complex / regulation of microtubule-based process / ErbB-3 class receptor binding / motor neuron axon guidance ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / semaphorin receptor complex / regulation of microtubule-based process / ErbB-3 class receptor binding / motor neuron axon guidance / Sema4D induced cell migration and growth-cone collapse / neurotransmitter receptor localization to postsynaptic specialization membrane / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / neuromuscular junction development / ERBB2 Activates PTK6 Signaling / enzyme-linked receptor protein signaling pathway / positive regulation of Rho protein signal transduction / ERBB2-ERBB3 signaling pathway / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / positive regulation of transcription by RNA polymerase I / oligodendrocyte differentiation / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / positive regulation of protein targeting to membrane / regulation of angiogenesis / Schwann cell development / regulation of ERK1 and ERK2 cascade / coreceptor activity / Signaling by ERBB2 / transmembrane receptor protein tyrosine kinase activity / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / myelination / positive regulation of MAP kinase activity / GRB2 events in ERBB2 signaling / positive regulation of cell adhesion / SHC1 events in ERBB2 signaling / cellular response to epidermal growth factor stimulus / Downregulation of ERBB2:ERBB3 signaling / Constitutive Signaling by Overexpressed ERBB2 / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of epithelial cell proliferation / basal plasma membrane / positive regulation of translation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / Signaling by ERBB2 TMD/JMD mutants / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / Signaling by ERBB2 ECD mutants / receptor protein-tyrosine kinase / neuromuscular junction / cellular response to growth factor stimulus / peptidyl-tyrosine phosphorylation / Signaling by ERBB2 KD Mutants / receptor tyrosine kinase binding / epidermal growth factor receptor signaling pathway / ruffle membrane / Downregulation of ERBB2 signaling / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / presynaptic membrane / heart development / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protein tyrosine kinase activity / basolateral plasma membrane / early endosome / cell population proliferation / receptor complex / cell surface receptor signaling pathway / positive regulation of MAPK cascade
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 / : / 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 ...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 / : / 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 / : / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsBostrom, J.M. / Wiesmann, C. / Appleton, B.A.
CitationJournal: Science / Year: 2009
Title: Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site
Authors: Bostrom, J. / Yu, S.F. / Kan, D. / Appleton, B.A. / Lee, C.V. / Billeci, K. / Man, W. / Peale, F. / Ross, S. / Wiesmann, C. / Fuh, G.
History
DepositionNov 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 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: Receptor tyrosine-protein kinase erbB-2
H: Fab Fragment-Heavy Chain
L: Fab Fragment-Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,9466
Polymers117,3083
Non-polymers6383
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.324, 115.056, 208.171
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: Protein Receptor tyrosine-protein kinase erbB-2 / p185erbB2 / C-erbB-2 / NEU proto-oncogene / Tyrosine kinase-type cell surface receptor HER2 / MLN ...p185erbB2 / C-erbB-2 / NEU proto-oncogene / Tyrosine kinase-type cell surface receptor HER2 / MLN 19 / CD340 antigen


Mass: 68794.086 Da / Num. of mol.: 1 / Fragment: sequence database residues 23-646
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB2, HER2, NEU, NGL / Cell line (production host): Chinese Hamster Ovary / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P04626, receptor protein-tyrosine kinase
#2: Antibody Fab Fragment-Heavy Chain


Mass: 24557.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: PDB-3BDY
#3: Antibody Fab Fragment-Light Chain


Mass: 23956.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: PDB-3BDY
#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


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
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Crystals of the Fab/HER2 complex were obtained by mixing protein solution (11 mg/ml protein, 25 mM Tris-HCl pH 8 and 150 mM sodium chloride) with crystallization buffer containing 25% w/v ...Details: Crystals of the Fab/HER2 complex were obtained by mixing protein solution (11 mg/ml protein, 25 mM Tris-HCl pH 8 and 150 mM sodium chloride) with crystallization buffer containing 25% w/v PEG2000, 0.1M MES pH 6.5. Before data collection the crystals were flash frozen in liquid nitrogen with 20% Ethylene Glycol as cryo-protectant, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 34149 / Num. obs: 34149 / % possible obs: 100 % / Redundancy: 5.7 % / Rsym value: 0.095 / Χ2: 0.981 / Net I/σ(I): 18.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.8 % / Num. unique all: 3328 / Rsym value: 0.658 / Χ2: 0.895 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BDY

3bdy


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.886 / SU B: 34.265 / SU ML: 0.304 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.776 / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1711 5 %RANDOM
Rwork0.236 ---
obs0.222 33988 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.135 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---4.19 Å20 Å2
3---4.67 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7770 0 40 0 7810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228024
X-RAY DIFFRACTIONr_bond_other_d0.0010.025412
X-RAY DIFFRACTIONr_angle_refined_deg1.211.95810937
X-RAY DIFFRACTIONr_angle_other_deg0.8463.00813133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75651005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35724.138348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.444151253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4691544
X-RAY DIFFRACTIONr_chiral_restr0.070.21208
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028949
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021568
X-RAY DIFFRACTIONr_nbd_refined0.2070.21530
X-RAY DIFFRACTIONr_nbd_other0.1850.25586
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23800
X-RAY DIFFRACTIONr_nbtor_other0.0830.24331
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1640.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2960.22
X-RAY DIFFRACTIONr_mcbond_it2.7282.55401
X-RAY DIFFRACTIONr_mcbond_other0.4642.52052
X-RAY DIFFRACTIONr_mcangle_it4.22758131
X-RAY DIFFRACTIONr_scbond_it2.4022.53291
X-RAY DIFFRACTIONr_scangle_it3.74152806
LS refinement shellResolution: 2.9→2.959 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.405 102 -
Rwork0.376 1850 -
all-1952 -
obs--97.36 %
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)
13.1396-0.41942.14761.21770.3573.0757-0.29680.21120.1829-0.23070.15030.1922-0.38320.01430.14650.21730.0147-0.0039-0.02050.0388-0.154729.7944-19.499186.4199
25.38154.23041.46823.32791.10941.2477-0.6556-0.20770.9928-0.3479-0.06270.7108-0.93710.02920.71840.61420.1456-0.4472-0.4985-0.03290.521730.977411.117296.6333
32.11780.94182.01062.88661.89683.20550.18940.0139-0.04460.07920.01340.0244-0.10640.143-0.20280.1548-0.00090.07230.01960.0085-0.174743.8698-21.1832103.6787
40.3428-1.07050.59643.3432-1.86271.0378-0.2965-0.1750.3310.2064-0.04930.693-0.4743-0.18290.34580.55110.3969-0.2773-0.1081-0.59220.5129.713812.3864113.428
52.08760.09110.34191.03650.04110.1507-0.06030.2082-0.0122-0.01850.0617-0.0109-0.02510.0205-0.0014-0.0267-0.0207-0.01190.02880.0310.0788-22.0268-24.826139.5992
60.3893-0.15930.25492.07570.35310.271-0.09120.00550.06910.22030.08440.0127-0.0053-0.02220.0068-0.01970.02310.0062-0.0150.00160.1375-7.966-7.385957.0914
71.30970.3309-0.14911.1772-0.18270.5752-0.02550.052-0.06330.12220.0517-0.0810.0235-0.0049-0.0262-0.01240.01-0.0567-0.0328-0.02450.12447.0973-38.721751.6103
82.59720.79312.49350.71910.83392.40490.12910.2237-0.17030.25050.22940.05610.21360.2414-0.35850.17320.1355-0.09480.0523-0.1061-0.08528.3618-45.065182.0399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1HB1 - 1144 - 122
2X-RAY DIFFRACTION2HB115 - 215123 - 223
3X-RAY DIFFRACTION3LC1 - 1091 - 113
4X-RAY DIFFRACTION4LC110 - 212114 - 216
5X-RAY DIFFRACTION5AA1 - 1951 - 195
6X-RAY DIFFRACTION6AA196 - 320196 - 320
7X-RAY DIFFRACTION6AD10011
8X-RAY DIFFRACTION7AA321 - 488321 - 488
9X-RAY DIFFRACTION8AA489 - 607489 - 607
10X-RAY DIFFRACTION8AE10021

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