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- EMDB-7012: Human alpha-V beta-3 Integrin (intermediate conformation) in comp... -

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Entry
Database: EMDB / ID: 7012
TitleHuman alpha-V beta-3 Integrin (intermediate conformation) in complex with the therapeutic antibody LM609
SampleQuaternary complex of human alpha-V beta-3 integrin with the Fab LM609
SourceHomo sapiens / human
Map dataHuman alpha-V beta-3 Integrin (intermediate conformation) in complex with the therapeutic antibody LM609
Methodsingle particle reconstruction, at 35 Å resolution
AuthorsBorst AJ / James ZN
CitationStructure, 2017, 25, 1732-1739.e5

Structure, 2017, 25, 1732-1739.e5 Yorodumi Papers
The Therapeutic Antibody LM609 Selectively Inhibits Ligand Binding to Human αVβ3 Integrin via Steric Hindrance.
Andrew J Borst / Zachary M James / William N Zagotta / Mark Ginsberg / Felix A Rey / Frank DiMaio / Marija Backovic / David Veesler

Validation ReportPDB-ID: 6avr

SummaryFull reportAbout validation report
DateDeposition: Sep 4, 2017 / Header (metadata) release: Nov 1, 2017 / Map release: Nov 1, 2017 / Last update: Nov 15, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.8
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 3.8
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6avr
  • Surface level: 3.8
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_7012.map.gz (map file in CCP4 format, 11944 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
144 pix
3.21 Å/pix.
= 461.578 Å
144 pix
3.21 Å/pix.
= 461.578 Å
144 pix
3.21 Å/pix.
= 461.578 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.2054 Å
Density
Contour Level:3.8 (by author), 3.8 (movie #1):
Minimum - Maximum-14.180465 - 32.64169
Average (Standard dev.)0.06803627 (0.9626198)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions144144144
Origin-72-72-72
Limit717171
Spacing144144144
CellA=B=C: 461.5776 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.20540277777783.20540277777783.2054027777778
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z461.578461.578461.578
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-14.18032.6420.068

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Supplemental data

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Sample components

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Entire Quaternary complex of human alpha-V beta-3 integrin with the Fab LM609

EntireName: Quaternary complex of human alpha-V beta-3 integrin with the Fab LM609
Number of components: 5
MassTheoretical: 230 kDa

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Component #1: protein, Quaternary complex of human alpha-V beta-3 integrin with...

ProteinName: Quaternary complex of human alpha-V beta-3 integrin with the Fab LM609
Recombinant expression: No
MassTheoretical: 230 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Drosophila melanogaster / arthropod / キイロショウジョウバエ /

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Component #2: protein, Integrin alpha-V

ProteinName: Integrin alpha-V / Recombinant expression: No
MassTheoretical: 105.894188 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #3: protein, Integrin beta-3

ProteinName: Integrin beta-3 / Recombinant expression: No
MassTheoretical: 76.523125 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #4: protein, Fab LM609 heavy chain

ProteinName: Fab LM609 heavy chain / Recombinant expression: No
MassTheoretical: 27.2231 kDa
Source (engineered)Expression System: Mus musculus / mammal / ハツカネズミ, はつかねずみ /

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Component #5: protein, Fab LM609 light chain

ProteinName: Fab LM609 light chain / Recombinant expression: No
MassTheoretical: 23.628977 kDa
Source (engineered)Expression System: Mus musculus / mammal / ハツカネズミ, はつかねずみ /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 8
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 650
3D reconstructionResolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF

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Atomic model buiding

Output model

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External links: The 2017 Nobel Prize in Chemistry - Press Release

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