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- PDB-6dlw: Complement component polyC9 -

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Basic information

Entry
Database: PDB / ID: 6dlw
TitleComplement component polyC9
ComponentsComplement component C9
KeywordsIMMUNE SYSTEM / Complement / pore / EM / membrane / transmembrane
Function / homologyMembrane attack complex component/perforin domain, conserved site / Thrombospondin type 1 domain / Membrane attack complex component/perforin (MACPF) domain / Thrombospondin type-1 (TSP1) repeat superfamily / Growth factor receptor cysteine-rich domain superfamily / Low-density lipoprotein (LDL) receptor class A repeat / Membrane attack complex component/perforin/complement C9 / Thrombospondin type-1 (TSP1) repeat / Complement component C9 / Low-density lipoprotein receptor domain class A ...Membrane attack complex component/perforin domain, conserved site / Thrombospondin type 1 domain / Membrane attack complex component/perforin (MACPF) domain / Thrombospondin type-1 (TSP1) repeat superfamily / Growth factor receptor cysteine-rich domain superfamily / Low-density lipoprotein (LDL) receptor class A repeat / Membrane attack complex component/perforin/complement C9 / Thrombospondin type-1 (TSP1) repeat / Complement component C9 / Low-density lipoprotein receptor domain class A / MAC/Perforin domain / LDL receptor-like superfamily / EGF-like domain signature 1. / Membrane attack complex/perforin (MACPF) domain signature. / EGF-like domain signature 2. / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Thrombospondin type-1 (TSP1) repeat profile. / Membrane attack complex/perforin (MACPF) domain profile. / Terminal pathway of complement / Regulation of Complement cascade / Low-density lipoprotein (LDL) receptor class A, conserved site / cell killing / membrane attack complex / complement activation, alternative pathway / hemolysis by symbiont of host erythrocytes / other organism cell membrane / complement activation, classical pathway / regulation of complement activation / protein homooligomerization / blood microparticle / integral component of plasma membrane / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol / Complement component C9
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsDunstone, M.A. / Spicer, B.A. / Law, R.H.P.
CitationJournal: Nat Commun / Year: 2018
Title: The first transmembrane region of complement component-9 acts as a brake on its self-assembly.
Authors: Bradley A Spicer / Ruby H P Law / Tom T Caradoc-Davies / Sue M Ekkel / Charles Bayly-Jones / Siew-Siew Pang / Paul J Conroy / Georg Ramm / Mazdak Radjainia / Hariprasad Venugopal / James C Whisstock / Michelle A Dunstone
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 3, 2018 / Release: Sep 12, 2018

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Complement component C9
B: Complement component C9
C: Complement component C9
D: Complement component C9
E: Complement component C9
F: Complement component C9
G: 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
P: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,352,07566
Polyers1,343,24522
Non-polymers8,83044
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)178670
ΔGint (kcal/M)-80
Surface area (Å2)458990

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Components

#1: Protein/peptide ...
Complement component C9 /


Mass: 61056.594 Da / Num. of mol.: 22 / Source: (gene. exp.) Homo sapiens (human) / Gene: C9 / Production host: Homo sapiens (human) / References: UniProt: P02748
#2: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 22 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical...
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 22 / 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

ComponentName: complement component polyC9 / Type: COMPLEX
Details: PolyC9 component of the membrane attack complex (MAC)
Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 1100 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer ID
110 mMHEPES1
250 mMSodium chloride1
SpecimenConc.: 1.3 mg/ml / Details: The sample was monodisperse / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Negative glow discharge / Grid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins / Details: blot for 2 seconds before plunging

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 8 sec. / Electron dose: 46.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
10EMAN2initial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C22
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 58000 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT

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