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- PDB-6avr: Human alpha-V beta-3 Integrin (intermediate conformation) in comp... -

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Database: PDB / ID: 6avr
TitleHuman alpha-V beta-3 Integrin (intermediate conformation) in complex with the therapeutic antibody LM609
DescriptorIntegrin alpha-V
Integrin beta-3
(Fab LM609 ...) x 2
KeywordsSIGNALING PROTEIN / alpha-V beta-3 integrin / LM609 / vitaxin / abegrin
Specimen sourceHomo sapiens / human
Mus musculus / mammal / ハツカネズミ, はつかねずみ /
MethodElectron microscopy (35 Å resolution / Particle / Single particle)
AuthorsBorst, A.J. / James, Z.N. / Zagotta, W.N. / Ginsberg, M. / Rey, F.A. / DiMaio, F. / Backovic, M. / Veesler, D.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Sep 4, 2017 / Release: Nov 1, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 1, 2017Structure modelrepositoryInitial release
1.1Nov 15, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Deposited unit
A: Integrin alpha-V
B: Integrin beta-3
H: Fab LM609 heavy chain
L: Fab LM609 light chain

Theoretical massNumber of molelcules
Total (without water)233,2694

TypeNameSymmetry operationNumber
identity operation1_5551


#1: Polypeptide(L)Integrin alpha-V / Vitronectin receptor / Vitronectin receptor subunit alpha

Mass: 105894.188 Da / Num. of mol.: 1 / Fragment: UNP residues 31-987 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P06756
#2: Polypeptide(L)Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa

Mass: 76523.125 Da / Num. of mol.: 1 / Fragment: UNP residues 27-718 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P05106
#3: Polypeptide(L)Fab LM609 heavy chain

Mass: 27223.100 Da / Num. of mol.: 1
Source: (gene. exp.) Mus musculus / mammal / ハツカネズミ, はつかねずみ /
#4: Polypeptide(L)Fab LM609 light chain

Mass: 23628.977 Da / Num. of mol.: 1
Source: (gene. exp.) Mus musculus / mammal / ハツカネズミ, はつかねずみ /

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Quaternary complex of human alpha-V beta-3 integrin with the Fab LM609
Type: COMPLEX / Entity ID: 1, 2, 3, 4 / Source: RECOMBINANT
Molecular weightValue: 0.23 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: Drosophila melanogaster
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl formate
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat 2/0.5

Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI 12
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)


EM software
IDNameCategoryFitting ID
CTF correctionType: NONE
3D reconstructionResolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 650 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL

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