[English] 日本語
Yorodumi
- PDB-3be1: Dual specific bH1 Fab in complex with the extracellular domain of... -

+
Open data


ID or keywords:

Loading...

-
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 / RNA polymerase I core binding / immature T cell proliferation in thymus / 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 / RNA polymerase I core binding / immature T cell proliferation in thymus / 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 / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / ERBB2 Activates PTK6 Signaling / neurotransmitter receptor localization to postsynaptic specialization membrane / enzyme-linked receptor protein signaling pathway / neuromuscular junction development / 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 MAP kinase activity / positive regulation of transcription by RNA polymerase I / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / oligodendrocyte differentiation / PI3K events in ERBB2 signaling / positive regulation of protein targeting to membrane / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / Schwann cell development / coreceptor activity / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / myelination / transmembrane receptor protein tyrosine kinase activity / GRB2 events in ERBB2 signaling / positive regulation of cell adhesion / SHC1 events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / cell surface receptor protein tyrosine kinase signaling pathway / basal plasma membrane / Constitutive Signaling by Overexpressed ERBB2 / cellular response to epidermal growth factor stimulus / peptidyl-tyrosine phosphorylation / positive regulation of translation / positive regulation of epithelial cell proliferation / neuromuscular junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / Signaling by ERBB2 TMD/JMD mutants / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / receptor tyrosine kinase binding / Signaling by ERBB2 KD Mutants / cellular response to growth factor stimulus / ruffle membrane / 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 / myelin sheath / heart development / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / protein tyrosine kinase activity / basolateral plasma membrane / early endosome / cell surface receptor signaling pathway / cell population proliferation / protein phosphorylation / receptor complex / endosome membrane / positive regulation of MAPK cascade / intracellular signal transduction / apical plasma membrane / protein heterodimerization activity / signaling receptor binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol
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 / Alpha-Beta Horseshoe / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV ...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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more