[English] 日本語
Yorodumi- PDB-8to9: Cryo-EM structure of TRNM-f*01 Fab in complex with HIV-1 Env trim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8to9 | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Antibody / Vaccination / VIRAL PROTEIN / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Biological species | Homo sapiens (human) Macaca mulatta (Rhesus monkey) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.03 Å | ||||||
Authors | Roark, R.S. / Morano, N.C. / Shapiro, L.S. / Kwong, P.D. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Broad and potent HIV-1 neutralization in fusion peptide-primed SHIV-boosted macaques Authors: Wang, H. / Kwong, P.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8to9.cif.gz | 419 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8to9.ent.gz | 351 KB | Display | PDB format |
PDBx/mmJSON format | 8to9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8to9_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8to9_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8to9_validation.xml.gz | 74.5 KB | Display | |
Data in CIF | 8to9_validation.cif.gz | 109.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/8to9 ftp://data.pdbj.org/pub/pdb/validation_reports/to/8to9 | HTTPS FTP |
-Related structure data
Related structure data | 41440MC 8tdxC 8tnuC 8to7C M: map data used to model this data C: citing same article (ref.) |
---|
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Envelope glycoprotein ... , 2 types, 6 molecules ABCIJZ
#1: Protein | Mass: 52737.102 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Protein | Mass: 17174.447 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
---|
-Antibody , 2 types, 6 molecules DEHFGL
#2: Antibody | Mass: 13923.301 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) #3: Antibody | Mass: 11464.811 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) |
---|
-Sugars , 3 types, 60 molecules
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
---|---|
Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 / Details: PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97698 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 187.09 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
|