[English] 日本語
Yorodumi
- PDB-6mhg: Cryo-EM structure of the circumsporozoite protein of Plasmodium f... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6mhg
TitleCryo-EM structure of the circumsporozoite protein of Plasmodium falciparum with a vaccine-elicited antibody reveals maturation of inter-antibody contacts
Components
  • Fab311 heavy chain
  • Fab311 light chain
  • circumsporozoite protein
KeywordsIMMUNE SYSTEM / Plasmodium falciparum / antibody / CSP / rsCSP
Function / homologyImmunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set / Immunoglobulin subtype / Immunoglobulin-like domain / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Immunoglobulin C1-set domain / Immunoglobulin V-set domain / Immunoglobulins and major histocompatibility complex proteins signature. ...Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set / Immunoglobulin subtype / Immunoglobulin-like domain / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Immunoglobulin C1-set domain / Immunoglobulin V-set domain / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Epididymis luminal protein 214
Function and homology information
Specimen sourcePlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.57 Å resolution
AuthorsCottrell, C.A. / Torres, J.L. / Ward, A.B.
CitationJournal: Sci Adv / Year: 2018
Title: Cryo-EM structure of circumsporozoite protein with a vaccine-elicited antibody is stabilized by somatically mutated inter-Fab contacts.
Authors: David Oyen / Jonathan L Torres / Christopher A Cottrell / C Richter King / Ian A Wilson / Andrew B Ward
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 17, 2018 / Release: Oct 31, 2018

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9114
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: circumsporozoite protein
H: Fab311 heavy chain
L: Fab311 light chain
A: Fab311 heavy chain
N: Fab311 light chain
B: Fab311 heavy chain
O: Fab311 light chain
C: Fab311 heavy chain
P: Fab311 light chain
D: Fab311 heavy chain
Q: Fab311 light chain
F: Fab311 heavy chain
R: Fab311 light chain
G: Fab311 heavy chain
S: Fab311 light chain
I: Fab311 heavy chain
T: Fab311 light chain
J: Fab311 heavy chain
U: Fab311 light chain
K: Fab311 heavy chain
V: Fab311 light chain
M: Fab311 heavy chain
W: Fab311 light chain


Theoretical massNumber of molelcules
Total (without water)548,10523
Polyers548,10523
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)41410
ΔGint (kcal/M)-173
Surface area (Å2)102980

-
Components

#1: Protein/peptide circumsporozoite protein


Mass: 30232.156 Da / Num. of mol.: 1 / Fragment: shortened construct
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli)
#2: Protein/peptide
Fab311 heavy chain


Mass: 24098.877 Da / Num. of mol.: 11 / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: V9HW68
#3: Protein/peptide
Fab311 light chain


Mass: 22980.484 Da / Num. of mol.: 11 / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Fab311 in complex with Plasmodium falciparum recombinant shortened CSPCOMPLEX1, 2, 30MULTIPLE SOURCES
2Plasmodium falciparum recombinant shortened CSPCOMPLEX11RECOMBINANT
3Fab311COMPLEX2, 31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
125833Plasmodium falciparum (malaria parasite P. falciparum)
239606Homo sapiens (human)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
12562Escherichia coli (E. coli)
239606Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins

-
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 / Nominal magnification: 29000 / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 62 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1497
Image scansSampling size: 5 microns / Width: 3710 / Height: 3838 / Movie frames/image: 48 / Used frames/image: 0-47

-
Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2Leginonimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9RosettaEMmodel refinement
12cryoSPARCclassification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 312806
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 206990 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL / Target criteria: EMRinger
Atomic model building
IDPDB-IDPdb chain ID 3D fitting ID
16AXKA1
26AXKB1
36AXKE1

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more