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Yorodumi- EMDB-18190: Cryo-EM map of the trastuzumab-HER2 complex obtained from local r... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18190 | |||||||||
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Title | Cryo-EM map of the trastuzumab-HER2 complex obtained from local refinement of the HER2-pertuzumab-trastuzumab ternary complex | |||||||||
Map data | Cryo-EM map of the trastuzumab-HER2 interface obtained my local refinement of the ternary complex HER2-pertuzumab-trastuzumab Fabs | |||||||||
Sample |
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Keywords | ErbB-2 / Trastuzumab / Ternary complex / Protein / Flexibility / Continuous conformation / Cryo-EM / Single particle analysis / Structural protein | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.33 Å | |||||||||
Authors | Ruedas R / Bressanelli S | |||||||||
Funding support | France, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18190.map.gz | 42.3 MB | EMDB map data format | |
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Header (meta data) | emd-18190-v30.xml emd-18190.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18190_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_18190.png | 116 KB | ||
Others | emd_18190_half_map_1.map.gz emd_18190_half_map_2.map.gz | 77.8 MB 77.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18190 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18190 | HTTPS FTP |
-Validation report
Summary document | emd_18190_validation.pdf.gz | 682.4 KB | Display | EMDB validaton report |
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Full document | emd_18190_full_validation.pdf.gz | 681.9 KB | Display | |
Data in XML | emd_18190_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | emd_18190_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18190 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18190 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18190.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM map of the trastuzumab-HER2 interface obtained my local refinement of the ternary complex HER2-pertuzumab-trastuzumab Fabs | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_18190_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_18190_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of her2-trastuzumab-pertuzumab Fabs
Entire | Name: Ternary complex of her2-trastuzumab-pertuzumab Fabs |
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Components |
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-Supramolecule #1: Ternary complex of her2-trastuzumab-pertuzumab Fabs
Supramolecule | Name: 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) |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 171.364 KDa |
-Macromolecule #1: Receptor tyrosine-protein kinase HER2
Macromolecule | Name: Receptor tyrosine-protein kinase HER2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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) |
-Macromolecule #2: Trastuzumab Fab heavy chain
Macromolecule | Name: Trastuzumab Fab heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: EVQLVESGGG LVQPGGSLRL SCAASGFTFT DYTMDWVRQA PGKGLEWVAD VNPNSGGSI YNQRFKGRFT LSVDRSKNTL YLQMNSLRAE DTAVYYCARN L GPSFYFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KD YFPEPVT VSWNSGALTS ...String: EVQLVESGGG LVQPGGSLRL SCAASGFTFT DYTMDWVRQA PGKGLEWVAD VNPNSGGSI YNQRFKGRFT LSVDRSKNTL YLQMNSLRAE DTAVYYCARN L GPSFYFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KD YFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTY ICNVNH KPSNTKVDKK VEPKSC |
-Macromolecule #3: Trastuzumab Fab light chain
Macromolecule | Name: Trastuzumab Fab light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRASQDVN TAVAWYQQKP GKAPKLLIYS ASFLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYCQ QHYTTPPTFG Q GTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KV DNALQSG NSQESVTEQD ...String: DIQMTQSPSS LSASVGDRVT ITCRASQDVN TAVAWYQQKP GKAPKLLIYS ASFLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYCQ QHYTTPPTFG Q GTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KV DNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQG LSSPVT KSFNRGEC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.12 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film 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 beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: HELIUM |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |