+Open data
-Basic information
Entry | Database: PDB / ID: 9c7v | ||||||||||||
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Title | Structure of the human BOS:human EMC complex in GDN | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / membrane protein biogenesis / membrane protein complex | ||||||||||||
Function / homology | Function and homology information multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / tail-anchored membrane protein insertion into ER membrane ...multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / tail-anchored membrane protein insertion into ER membrane / Miscellaneous transport and binding events / ferrous iron transmembrane transporter activity / magnesium ion transmembrane transporter activity / copper ion transport / regulation of protein complex stability / autophagosome assembly / RHOA GTPase cycle / regulation of protein-containing complex assembly / regulation of signal transduction / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / positive regulation of angiogenesis / ribosome binding / early endosome membrane / carbohydrate binding / angiogenesis / membrane => GO:0016020 / early endosome / protein stabilization / Golgi membrane / endoplasmic reticulum membrane / apoptotic process / Golgi apparatus / endoplasmic reticulum / protein-containing complex / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å | ||||||||||||
Authors | Nguyen, V.N. / Tomaleri, G.P. / Voorhees, R.M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Role of a holo-insertase complex in the biogenesis of biophysically diverse ER membrane proteins Authors: Page, K.R. / Nguyen, V.N. / Pleiner, T. / Tomaleri, G.P. / Wang, M.L. / Guna, A. / Hazu, M. / Wang, T. / Chou, T. / Voorhees, R.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9c7v.cif.gz | 691.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c7v.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9c7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/9c7v ftp://data.pdbj.org/pub/pdb/validation_reports/c7/9c7v | HTTPS FTP |
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-Related structure data
Related structure data | 45295MC 9c7uC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-ER membrane protein complex subunit ... , 8 types, 8 molecules 101234678
#1: Protein | Mass: 27375.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5UCC4 |
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#2: Protein | Mass: 111886.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N766 |
#3: Protein | Mass: 34882.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EMC2, KIAA0103, TTC35 / Production host: Homo sapiens (human) / References: UniProt: Q15006 |
#4: Protein | Mass: 29981.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0I2 |
#5: Protein | Mass: 20104.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5J8M3 |
#7: Protein | Mass: 12029.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BV81 |
#8: Protein | Mass: 26501.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NPA0 |
#9: Protein | Mass: 23807.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43402 |
-Protein , 4 types, 4 molecules 5ABC
#6: Protein | Mass: 14706.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N4V1 |
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#10: Protein | Mass: 63047.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q969V3 |
#11: Protein | Mass: 139580.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5JPE7 |
#12: Protein | Mass: 25279.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM147 / Production host: Homo sapiens (human) / References: UniProt: Q9BVK8 |
-Sugars , 2 types, 4 molecules
#13: Polysaccharide | Source method: isolated from a genetically manipulated source #14: Sugar | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human BOS complex / Type: COMPLEX / Details: Human BOS complex of NOMO, TMEM147, and NCLN / Entity ID: #1-#12 / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2.53 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample solubilized and purified in GDN. | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 279 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: DARK FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17978 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45703 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 105.92 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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