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- PDB-3h3b: Crystal structure of the single-chain Fv (scFv) fragment of an an... -

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Basic information

Entry
Database: PDB / ID: 3h3b
TitleCrystal structure of the single-chain Fv (scFv) fragment of an anti-ErbB2 antibody chA21 in complex with residues 1-192 of ErbB2 extracellular domain
Components
  • Receptor tyrosine-protein kinase erbB-2
  • anti-ErbB2 antibody chA21
KeywordsIMMUNE SYSTEM / immunoglobulin / beta-helix / protein-protein complex / ATP-binding / Disulfide bond / Kinase / Nucleotide-binding / Receptor / Transferase / 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 / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse ...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 / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / neuromuscular junction development / positive regulation of Rho protein signal transduction / ERBB2 Activates PTK6 Signaling / 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 / enzyme-linked receptor protein signaling pathway / positive regulation of transcription by RNA polymerase I / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / positive regulation of cell adhesion / positive regulation of protein targeting to membrane / regulation of angiogenesis / coreceptor activity / Schwann cell development / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / myelination / Downregulation of ERBB2:ERBB3 signaling / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / neurogenesis / basal plasma membrane / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of translation / positive regulation of epithelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / wound healing / neuromuscular junction / Signaling by ERBB2 ECD mutants / neuron differentiation / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / cellular response to growth factor stimulus / Downregulation of ERBB2 signaling / ruffle membrane / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / presynaptic membrane / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / basolateral plasma membrane / protein tyrosine kinase activity / positive regulation of MAPK cascade / early endosome / cell surface receptor signaling pathway / receptor complex / endosome membrane / intracellular signal transduction / apical plasma membrane / positive regulation of protein phosphorylation / protein heterodimerization activity / protein phosphorylation / signaling receptor binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane
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
Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsZhou, H. / Liu, Y. / Niu, L. / Zhu, J. / Teng, M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Insights into the Down-regulation of Overexpressed p185her2/neu Protein of Transformed Cells by the Antibody chA21.
Authors: Zhou, H. / Zha, Z. / Liu, Y. / Zhang, H. / Zhu, J. / Hu, S. / Shen, G. / Cheng, L. / Niu, L. / Greene, M.I. / Teng, M. / Liu, J.
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 28, 2011Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor tyrosine-protein kinase erbB-2
B: Receptor tyrosine-protein kinase erbB-2
C: anti-ErbB2 antibody chA21
D: anti-ErbB2 antibody chA21


Theoretical massNumber of molelcules
Total (without water)98,4584
Polymers98,4584
Non-polymers00
Water4,306239
1
A: Receptor tyrosine-protein kinase erbB-2
C: anti-ErbB2 antibody chA21


Theoretical massNumber of molelcules
Total (without water)49,2292
Polymers49,2292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-7 kcal/mol
Surface area18700 Å2
MethodPISA
2
B: Receptor tyrosine-protein kinase erbB-2
D: anti-ErbB2 antibody chA21


Theoretical massNumber of molelcules
Total (without water)49,2292
Polymers49,2292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-7 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.177, 87.200, 108.520
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 19


Mass: 21669.643 Da / Num. of mol.: 2 / Fragment: extracellular domain, UNP residues 23-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB2 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B
References: UniProt: P04626, receptor protein-tyrosine kinase
#2: Antibody anti-ErbB2 antibody chA21


Mass: 27559.383 Da / Num. of mol.: 2 / Fragment: the single-chain Fv (scFv) fragment
Source method: isolated from a genetically manipulated source
Details: the scFv is derivated from A21 mAb(GeneBank Accession No. AY077780 for VH and AY077782 for VL), and constructed in VL-(Gly4Ser)4-VH mode.
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Gene: scFv of murine antibody A21 / Plasmid: pEE14 / Cell line (production host): CHO CELLS / Organ (production host): OVARY / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREGARDING CHAIN B, THIS CONSISTS OF THREE PART. N- AND C- TERMINAL REGION CAN BE REFERRED TO ...REGARDING CHAIN B, THIS CONSISTS OF THREE PART. N- AND C- TERMINAL REGION CAN BE REFERRED TO AY077782 AND AY077780 IN GENBANK, RESPECTIVELY. THE FIRST FIVE RESIDUES, AAQPA, ARE EXPRESSION TAGS AND RGGGGSGGGGSGGGGSGGGGS IN THE MIDDLE OF THE SEQUENCE ARE LINERER.

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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: 1.97 Å3/Da / Density % sol: 37.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% polyethylene glycol 4000, 100mM 3-(1-pyridino)-1-propane sulfonate, 100mM Na cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→29.91 Å / Num. obs: 29113 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.3
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4139

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2GJJ and 2A91

2gjj

2a91


Resolution: 2.45→29.91 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.891 / SU B: 18.834 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 2.064 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25542 1461 5 %RANDOM
Rwork0.20061 ---
obs0.20333 27646 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.493 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--0.44 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.45→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 0 239 6881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226730
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0371.9479170
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7045853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.6424.724290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.717151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3891529
X-RAY DIFFRACTIONr_chiral_restr0.080.21031
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025099
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1780.22776
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.24452
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2372
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3140.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2961.54240
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.4526839
X-RAY DIFFRACTIONr_scbond_it0.39532490
X-RAY DIFFRACTIONr_scangle_it0.6874.52325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 102 -
Rwork0.251 1955 -
obs--97.58 %
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)
13.27190.19430.9152.93394.486610.0457-0.053-0.1403-0.76050.17920.05390.06950.85110.1357-0.0009-0.0107-0.0440.07930.02520.0030.161410.8695-27.9609-19.7541
22.228-0.26110.60722.72520.40962.1736-0.03530.0179-0.1257-0.12340.04760.03610.06180.0246-0.01230.0085-0.01690.04150.0773-0.02130.064812.5391-17.6572-19.7742
34.12-0.14941.81271.4314-0.18342.52480.00050.0564-0.2249-0.03560.1014-0.08980.02440.1167-0.10190.0213-0.0290.0530.0134-0.01870.101921.2476-10.4264-16.1508
44.93460.7130.96231.29780.44772.4340.01480.40430.3465-0.23060.04150.1368-0.1172-0.0472-0.05630.03690.00420.00570.00530.00730.093718.3888-3.3604-21.6173
54.33320.7873-2.15193.3986-2.48776.1998-0.17010.3239-0.75240.0472-0.0056-0.44070.5819-0.210.1757-0.0409-0.0071-0.04480.0305-0.10470.217325.1639-32.62788.3968
64.16641.52962.29553.66810.15352.71940.1838-0.1302-0.31630.28460.0474-0.20780.0536-0.0673-0.23120.01580.0425-0.0050.0141-0.0370.130723.8849-24.174312.6869
72.6343-0.76130.3851.06-0.0651.62680.0401-0.1394-0.09780.14650.0413-0.0919-0.02830.0229-0.08140.0485-0.0113-0.00140.03040.01230.087319.4729-12.254611.6368
89.1685-1.3201-3.17590.4762-0.64075.3124-0.2664-1.590.26781.0340.3784-0.1074-0.7356-0.3229-0.1120.4384-0.0556-0.22530.07090.05240.036910.4024-12.195222.4396
92.90281.1994-0.36633.87281.1382.149-0.0515-0.0963-0.0614-0.06810.0589-0.0631-0.04640.2111-0.0074-0.0252-0.0020.05810.067-0.00960.02449.80553.2236-17.1994
101.84651.0805-1.05292.1005-0.75862.94920.1269-0.07040.3750.02810.04120.1858-0.30150.1198-0.16810.0267-0.00070.03430.0338-0.04750.13646.159710.4416-13.8275
112.66460.44350.07083.25220.37832.59650.0899-0.35010.24420.222-0.10620.102-0.12250.07020.0163-0.0211-0.04080.05380.1239-0.08710.046137.30482.86272.6487
122.82410.83321.01771.61810.85564.54550.1517-0.35140.16530.2343-0.0748-0.0033-0.05040.2406-0.0769-0.0272-0.04110.04180.032-0.07470.060539.05112.4892.4797
133.1389-0.25440.78723.54260.79433.99730.0015-0.1468-0.44090.2186-0.19450.6626-0.1217-0.63590.1930.0207-0.0210.14760.11210.0159-0.0529-14.78981.237915.766
142.6737-0.6622-0.84782.27060.63774.3692-0.013-0.11160.20240.490.01310.219-0.4683-0.1825-0.00010.14790.03110.047-0.0107-0.0031-0.0288-7.39138.002714.2155
151.561-0.48230.28762.4273-0.90591.4593-0.03210.21740.0746-0.1507-0.0823-0.0794-0.0043-0.07790.11440.0439-0.00110.00160.0975-0.00860.01940.12295.1209-3.432
161.452-1.0096-0.12842.5957-1.39851.52420.05480.196-0.1027-0.03360.00860.1336-0.02770.0023-0.06340.02890.009-0.00850.0558-0.0140.0049-1.36323.5679-3.4284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 32
2X-RAY DIFFRACTION2A33 - 98
3X-RAY DIFFRACTION3A99 - 146
4X-RAY DIFFRACTION4A147 - 192
5X-RAY DIFFRACTION5B0 - 31
6X-RAY DIFFRACTION6B32 - 88
7X-RAY DIFFRACTION7B89 - 171
8X-RAY DIFFRACTION8B172 - 191
9X-RAY DIFFRACTION9C-2 - 43
10X-RAY DIFFRACTION10C44 - 138
11X-RAY DIFFRACTION11C139 - 194
12X-RAY DIFFRACTION12C195 - 253
13X-RAY DIFFRACTION13D-2 - 34
14X-RAY DIFFRACTION14D35 - 140
15X-RAY DIFFRACTION15D141 - 190
16X-RAY DIFFRACTION16D191 - 253

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