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- EMDB-18189: Cryo-EM map of the pertuzumab-HER2 complex obtained from local re... -

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Basic information

Entry
Database: EMDB / ID: EMD-18189
TitleCryo-EM map of the pertuzumab-HER2 complex obtained from local refinement of the HER2-pertuzumab-trastuzumab ternary complex
Map dataMap showing the pertuzumab-HER2 interface obtained by local refinement.
Sample
  • Complex: Ternary complex of her2-trastuzumab-pertuzumab Fabs
    • Protein or peptide: Receptor tyrosine-protein kinase HER2
    • Protein or peptide: Pertuzumab Fab heavy chain
    • Protein or peptide: Pertuzumab light chain
KeywordsErbB-2 / Pertuzumab / Ternary complex / Protein / Flexibility / Continuous conformation / Cryo-EM / Single particle analysis / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsRuedas R / Bressanelli S
Funding support France, 2 items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
Other private
CitationJournal: To Be Published
Title: Atomic structure and conformational variability of the HER2-Trastuzumab-Pertuzumab complex
Authors: Ruedas R / Vuillemot R / Tubiana T / Winter JM / Pieri L / Arteni AA / Samson C / Jonic J / Mathieu M / Bressanelli S
History
DepositionAug 11, 2023-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18189.png

Downloads & links

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Map

FileDownload / File: emd_18189.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap showing the pertuzumab-HER2 interface obtained by local refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 280 pix.
= 324.8 Å		1.16 Å/pix.
x 280 pix.
= 324.8 Å		1.16 Å/pix.
x 280 pix.
= 324.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-0.8378597 - 1.3562968
Average (Standard dev.)0.00039681816 (±0.021162177)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 324.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_18189_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_18189_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of her2-trastuzumab-pertuzumab Fabs

EntireName: Ternary complex of her2-trastuzumab-pertuzumab Fabs
Components
  • Complex: Ternary complex of her2-trastuzumab-pertuzumab Fabs
    • Protein or peptide: Receptor tyrosine-protein kinase HER2
    • Protein or peptide: Pertuzumab Fab heavy chain
    • Protein or peptide: Pertuzumab light chain

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Supramolecule #1: Ternary complex of her2-trastuzumab-pertuzumab Fabs

SupramoleculeName: Ternary complex of her2-trastuzumab-pertuzumab Fabs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Fab fragment from trastuzumab and pertuzumab linked to the extracellular domain of erbb2 (her2)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 171.364 KDa

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Macromolecule #1: Receptor tyrosine-protein kinase HER2

MacromoleculeName: Receptor tyrosine-protein kinase HER2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TQVCTGTDMK LRLPASPETH LDMLRHLYQG CQVVQGNLEL TYLPTNASLS FLQDIQEVQG YVLIAHNQVR QVPLQRLRIV RGTQLFEDN YALAVLDNGD PLNNTTPVTG ASPGGLRELQ LRSLTEILKG GVLIQRNPQL CYQDTILWKD IFHKNNQLAL T LIDTNRSR ...String:
TQVCTGTDMK LRLPASPETH LDMLRHLYQG CQVVQGNLEL TYLPTNASLS FLQDIQEVQG YVLIAHNQVR QVPLQRLRIV RGTQLFEDN YALAVLDNGD PLNNTTPVTG ASPGGLRELQ LRSLTEILKG GVLIQRNPQL CYQDTILWKD IFHKNNQLAL T LIDTNRSR ACHPCSPMCK GSRCWGESSE DCQSLTRTVC AGGCARCKGP LPTDCCHEQC AAGCTGPKHS DCLACLHFNH SG ICELHCP ALVTYNTDTF ESMPNPEGRY TFGASCVTAC PYNYLSTDVG SCTLVCPLHN QEVTAEDGTQ RCEKCSKPCA RVC YGLGME HLREVRAVTS ANIQEFAGCK KIFGSLAFLP ESFDGDPASN TAPLQPEQLQ VFETLEEITG YLYISAWPDS LPDL SVFQN LQVIRGRILH NGAYSLTLQG LGISWLGLRS LRELGSGLAL IHHNTHLCFV HTVPWDQLFR NPHQALLHTA NRPED ECVG EGLACHQLCA RGHCWGPGPT QCVNCSQFLR GQECVEECRV LQGLPREYVN ARHCLPCHPE CQPQNGSVTC FGPEAD QCV ACAHYKDPPF CVARCPSGVK PDLSYMPIWK FPDEEGACQP CPINCTHSCV DLDDKGCPAE Q(NAG)(NAG)(NAG)(BMA)(NAG)(NAG)(BMA)(NAG)(NAG)

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Macromolecule #2: Pertuzumab Fab heavy chain

MacromoleculeName: Pertuzumab Fab heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFNIK DTYIHWVRQA PGKGLEWVAR IYPTNGYTR YADSVKGRFT ISADTSKNTA YLQMNSLRAE DTAVYYCSRW G GDGFYAMD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VK DYFPEPV TVSWNSGALT ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFNIK DTYIHWVRQA PGKGLEWVAR IYPTNGYTR YADSVKGRFT ISADTSKNTA YLQMNSLRAE DTAVYYCSRW G GDGFYAMD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VK DYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQT YICNVN HKPSNTKVDK KVEP

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Macromolecule #3: Pertuzumab light chain

MacromoleculeName: Pertuzumab light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCKASQDVS IGVAWYQQKP GKAPKLLIYS ASYRYTGVP SRFSGSGSGT DFTLTISSLQ PEDFATYYCQ QYYIYPYTFG Q GTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KV DNALQSG NSQESVTEQD ...String:
DIQMTQSPSS LSASVGDRVT ITCKASQDVS IGVAWYQQKP GKAPKLLIYS ASYRYTGVP SRFSGSGSGT DFTLTISSLQ PEDFATYYCQ QYYIYPYTFG Q GTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KV DNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQG LSSPVT KSFNRGEC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.12 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 8928 / Average exposure time: 4.71 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 240000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: HELIUM

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Image processing

Particle selectionNumber selected: 2954825
Startup modelType of model: OTHER
Details: 6oge, 1z8z and 1s78 pdb were used to build the startup model.
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 711008
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainPDB ID
source_name: AlphaFold, initial_model_type: in silico model
source_name: PDB, initial_model_type: experimental model

1n8z

chain_id: C, source_name: PDB, initial_model_type: experimental model

1s78

chain_id: D, source_name: PDB, initial_model_type: experimental model

1s78

source_name: PDB, initial_model_type: experimental model

6oge

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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