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- PDB-6h03: OPEN CONFORMATION OF THE MEMBRANE ATTACK COMPLEX -

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Entry
Database: PDB / ID: 6h03
TitleOPEN CONFORMATION OF THE MEMBRANE ATTACK COMPLEX
Components
  • (Complement component ...) x 6
  • Complement C5,Complement C5
KeywordsIMMUNE SYSTEM / C5B9
Function / homologyMacroglobulin domain MG3 / Complement component C6 / Alpha-2-macroglobulin family / Thrombospondin type 1 domain / Sushi repeat (SCR repeat) / Lipocalin / cytosolic fatty-acid binding protein family / Low-density lipoprotein receptor domain class A / Kazal-type serine protease inhibitor domain / Complement component C9 / Complement component C8 beta chain ...Macroglobulin domain MG3 / Complement component C6 / Alpha-2-macroglobulin family / Thrombospondin type 1 domain / Sushi repeat (SCR repeat) / Lipocalin / cytosolic fatty-acid binding protein family / Low-density lipoprotein receptor domain class A / Kazal-type serine protease inhibitor domain / Complement component C9 / Complement component C8 beta chain / Complement component C8 alpha chain / Complement component C7 / Complement C5 / Anaphylotoxin-like domain / Alpha-macroglobulin, receptor-binding domain superfamily / Thrombospondin type-1 (TSP1) repeat superfamily / LDL receptor-like superfamily / Sushi/SCR/CCP superfamily / Low-density lipoprotein (LDL) receptor class A, conserved site / Lipocalin family conserved site / Membrane attack complex component/perforin (MACPF) domain / Membrane attack complex component/perforin domain, conserved site / Netrin module, non-TIMP type / Anaphylatoxin, complement system / Calycin / UNC-6/NTR/C345C module / MAC/Perforin domain / Alpha-2-macroglobulin, bait region domain / Thrombospondin type-1 (TSP1) repeat profile. / Macroglobulin domain MG1 / Macroglobulin domain MG4 / Regulation of Complement cascade / G alpha (i) signalling events / Peptide ligand-binding receptors / Activation of C3 and C5 / Terminal pathway of complement / Kazal domain profile. / Membrane attack complex/perforin (MACPF) domain profile. / Sushi/CCP/SCR domain profile. / NTR domain profile. / LDL-receptor class A (LDLRA) domain profile. / MG2 domain / LDL-receptor class A (LDLRA) domain signature. / EGF-like domain signature 2. / Anaphylatoxin domain profile. / Anaphylatoxin domain signature. / Membrane attack complex/perforin (MACPF) domain signature. / Lipocalin signature. / EGF-like domain signature 1. / Kazal-type serine protease inhibitor domain / Alpha-2-macroglobulin bait region domain / A-macroglobulin TED domain / A-macroglobulin receptor binding domain / Alpha-macroglobulin, TED domain / Immunoglobulin-like fold / Alpha-macroglobulin, receptor-binding / Membrane attack complex component/perforin/complement C9 / Growth factor receptor cysteine-rich domain superfamily / Anaphylatoxin/fibulin / Sushi/SCR/CCP domain / Lipocalin/cytosolic fatty-acid binding domain / Thrombospondin type-1 (TSP1) repeat / Netrin domain / Alpha-2-macroglobulin / Anaphylatoxin, complement system domain / Low-density lipoprotein (LDL) receptor class A repeat / Lipocalin / Kazal domain / Macroglobulin domain / Alpha-1-microglobulin / Factor I / membrane attack complex / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Tissue inhibitor of metalloproteinases-like, OB-fold / cell killing / membrane attack complex / complement binding / positive regulation of activation of membrane attack complex / cellular sodium ion homeostasis / positive regulation of chemokine secretion / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / other organism cell membrane / retinol binding / extracellular vesicle / positive regulation of vascular endothelial growth factor production / complement activation / regulation of complement activation / complement activation, classical pathway / positive regulation of angiogenesis / in utero embryonic development / chemotaxis / protein homooligomerization / activation of MAPK activity / cytolysis / cell surface receptor signaling pathway / blood microparticle / immune response / protein-containing complex binding
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5.6 Å resolution
AuthorsMenny, A. / Serna, M. / Boyd, C.M. / Gardner, S. / Joseph, A.P. / Topf, M. / Bubeck, D.
CitationJournal: Nat Commun / Year: 2018
Title: CryoEM reveals how the complement membrane attack complex ruptures lipid bilayers.
Authors: Anaïs Menny / Marina Serna / Courtney M Boyd / Scott Gardner / Agnel Praveen Joseph / B Paul Morgan / Maya Topf / Nicholas J Brooks / Doryen Bubeck
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 6, 2018 / Release: Dec 19, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 19, 2018Structure modelrepositoryInitial release
1.1Dec 26, 2018Structure modelAuthor supporting evidence / Data collection / Database referencescitation / citation_author / em_single_particle_entity_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_single_particle_entity.id

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-0106
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement C5,Complement C5
C: Complement component C8 beta chain
D: Complement component C7
E: Complement component C8 gamma chain
F: Complement component C8 alpha chain
B: Complement component C6
G: Complement component C9
P: Complement component C9
H: Complement component C9
I: Complement component C9
J: Complement component C9
K: Complement component C9
L: Complement component C9
M: Complement component C9
N: Complement component C9
O: Complement component C9
Q: Complement component C9
R: Complement component C9
S: Complement component C9
T: Complement component C9
U: Complement component C9
V: Complement component C9
W: Complement component C9
X: Complement component C9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,631,460104
Polyers1,613,80524
Non-polymers17,65680
Water0
1


  • idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)236580
ΔGint (kcal/M)-6
Surface area (Å2)626070
MethodPISA

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide Complement C5,Complement C5 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4


Mass: 177707.391 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P01031

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Complement component ... , 6 types, 23 molecules CDEFBGPHIJKLMNOQRSTUVWX

#2: Protein/peptide Complement component C8 beta chain / / Complement component 8 subunit beta


Mass: 61122.852 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P07358
#3: Protein/peptide Complement component C7 /


Mass: 91221.484 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P10643
#4: Protein/peptide Complement component C8 gamma chain /


Mass: 20410.105 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P07360
#5: Protein/peptide Complement component C8 alpha chain / / Complement component 8 subunit alpha


Mass: 61782.992 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P07357
#6: Protein/peptide Complement component C6 /


Mass: 102541.312 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P13671
#7: Protein/peptide
Complement component C9 /


Mass: 61056.594 Da / Num. of mol.: 18 / Source: (natural) Homo sapiens (human) / References: UniProt: P02748

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Non-polymers , 2 types, 80 molecules

#8: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 79 / Formula: C8H15NO6 / N-Acetylglucosamine
#9: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component

Source: NATURAL / Type: COMPLEX

IDNameDetailsEntity IDParent ID
1Membrane Attack ComplexProtein complex was assembled on liposomes and detergent solubilized1, 2, 3, 4, 5, 6, 70
2C5b11
3C661
4C731
5C8 alpha51
6C8 beta21
7C8 gamma41
8C971
Molecular weight
IDValueEntity assembly IDExperimental value
11.6 MDa1NO
20.18 MDa1NO
30.1 MDa1NO
40.09 MDa1NO
50.06 MDa1NO
60.06 MDa1NO
70.02 MDa1NO
80.069 MDa1NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
219606Homo sapiens (human)
329606Homo sapiens (human)
439606Homo sapiens (human)
549606Homo sapiens (human)
659606Homo sapiens (human)
769606Homo sapiens (human)
879606Homo sapiens (human)
989606Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 8 / Number of real images: 13009

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7Flex-EMmodel fitting
8Cootmodel fitting
9iMODFITmodel fitting
10MODELLERmodel fitting
11TEMPymodel fitting
12UCSF Chimeramodel fitting
14RELIONinitial Euler assignment
15RELIONfinal Euler assignment
16RELIONclassification
17RELION3D reconstruction
18PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 288366
SymmetryPoint symmetry: C1
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 81968 / Symmetry type: POINT
Least-squares processHighest resolution: 5.6 Å

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