[English] 日本語
Yorodumi- PDB-7jgh: Cryo-EM structure of P. falciparum VAR2CSA NF54 core in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jgh | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of P. falciparum VAR2CSA NF54 core in complex with CSA at 3.36 A | ||||||
Components | Erythrocyte membrane protein 1 | ||||||
Keywords | SUGAR BINDING PROTEIN / Placental malaria / VAR2CSA / Duffy binding domain / CSA / PfEMP1 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å | ||||||
Authors | Ma, R. / Tolia, N.H. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Nat Microbiol / Year: 2021 Title: Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA. Authors: Rui Ma / Tengfei Lian / Rick Huang / Jonathan P Renn / Jennifer D Petersen / Joshua Zimmerberg / Patrick E Duffy / Niraj H Tolia / Abstract: Plasmodium falciparum VAR2CSA binds to chondroitin sulfate A (CSA) on the surface of the syncytiotrophoblast during placental malaria. This interaction facilitates placental sequestration of malaria ...Plasmodium falciparum VAR2CSA binds to chondroitin sulfate A (CSA) on the surface of the syncytiotrophoblast during placental malaria. This interaction facilitates placental sequestration of malaria parasites resulting in severe health outcomes for both the mother and her offspring. Furthermore, CSA is presented by diverse cancer cells and specific targeting of cells by VAR2CSA may become a viable approach for cancer treatment. In the present study, we determined the cryo-electron microscopy structures of the full-length ectodomain of VAR2CSA from P. falciparum strain NF54 in complex with CSA, and VAR2CSA from a second P. falciparum strain FCR3. The architecture of VAR2CSA is composed of a stable core flanked by a flexible arm. CSA traverses the core domain by binding within two channels and CSA binding does not induce major conformational changes in VAR2CSA. The CSA-binding elements are conserved across VAR2CSA variants and are flanked by polymorphic segments, suggesting immune selection outside the CSA-binding sites. This work provides paths for developing interventions against placental malaria and cancer. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7jgh.cif.gz | 437.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7jgh.ent.gz | 355.1 KB | Display | PDB format |
PDBx/mmJSON format | 7jgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jgh_validation.pdf.gz | 911.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7jgh_full_validation.pdf.gz | 934.4 KB | Display | |
Data in XML | 7jgh_validation.xml.gz | 44.8 KB | Display | |
Data in CIF | 7jgh_validation.cif.gz | 66.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/7jgh ftp://data.pdbj.org/pub/pdb/validation_reports/jg/7jgh | HTTPS FTP |
-Related structure data
Related structure data | 22327MC 7jgdC 7jgeC 7jgfC 7jggC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 308706.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate NF54) (eukaryote) Strain: isolate NF54 / Gene: PFNF54_03544 / Production host: Homo sapiens (human) / References: UniProt: W7K270 |
---|---|
#2: Polysaccharide | beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta- ...beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-ASG / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: VAR2CSA NF54 core in complex with CSA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Plasmodium falciparum (isolate NF54) (eukaryote) / Strain: isolate NF54 |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 57 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 299571 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|