[English] 日本語
Yorodumi
- PDB-6o26: Crystal structure of 3246 Fab in complex with circumsporozoite pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o26
TitleCrystal structure of 3246 Fab in complex with circumsporozoite protein NANA
Components
  • 3246 Fab heavy chain
  • 3246 Fab light chain
  • Circumsporozoite protein
KeywordsIMMUNE SYSTEM / Malaria / antibody
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / external side of plasma membrane / cytoplasm
Similarity search - Function
: / Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsScally, S.W. / Bosch, A. / Castro, K. / Murugan, R. / Wardemann, H. / Julien, J.P.
Funding support1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation
CitationJournal: Nat. Med. / Year: 2020
Title: Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs.
Authors: Murugan, R. / Scally, S.W. / Costa, G. / Mustafa, G. / Thai, E. / Decker, T. / Bosch, A. / Prieto, K. / Levashina, E.A. / Julien, J.P. / Wardemann, H.
History
DepositionFeb 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3246 Fab heavy chain
B: 3246 Fab light chain
C: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6656
Polymers48,4213
Non-polymers2443
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-20 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.141, 68.682, 104.212
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

-
Components

-
Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Circumsporozoite protein / CS


Mass: 1486.482 Da / Num. of mol.: 1 / Fragment: residues 289-302 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P19597

-
Antibody , 2 types, 2 molecules AB

#1: Antibody 3246 Fab heavy chain


Mass: 23609.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 3246 Fab light chain


Mass: 23324.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Non-polymers , 4 types, 388 molecules

#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 % (v/v) isopropanol, 20 % (w/v) PEG4000, 0.1 M HEPES pH 7.5 and 10 % (w/v) ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 45439 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2139 / CC1/2: 0.532 / Rpim(I) all: 0.302 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.308 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.62
RfactorNum. reflection% reflection
Rfree0.207 2270 5 %
Rwork0.1632 --
obs0.1654 45390 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→35.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 16 385 3708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013396
X-RAY DIFFRACTIONf_angle_d1.1524612
X-RAY DIFFRACTIONf_dihedral_angle_d14.1072019
X-RAY DIFFRACTIONf_chiral_restr0.076513
X-RAY DIFFRACTIONf_plane_restr0.007593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83910.27251390.2422639X-RAY DIFFRACTION100
1.8391-1.88190.26921410.22962671X-RAY DIFFRACTION100
1.8819-1.9290.24781390.20372644X-RAY DIFFRACTION100
1.929-1.98110.27541390.20392667X-RAY DIFFRACTION100
1.9811-2.03940.2391410.17692681X-RAY DIFFRACTION100
2.0394-2.10520.22771400.17782649X-RAY DIFFRACTION100
2.1052-2.18050.2121410.16752681X-RAY DIFFRACTION100
2.1805-2.26780.22711400.17112652X-RAY DIFFRACTION100
2.2678-2.3710.2271410.17542679X-RAY DIFFRACTION100
2.371-2.49590.25061410.17272686X-RAY DIFFRACTION100
2.4959-2.65230.2171410.17262686X-RAY DIFFRACTION100
2.6523-2.8570.2241420.17092691X-RAY DIFFRACTION100
2.857-3.14430.21321430.1632720X-RAY DIFFRACTION100
3.1443-3.59890.17681440.1462726X-RAY DIFFRACTION100
3.5989-4.53270.16761450.13622758X-RAY DIFFRACTION100
4.5327-35.31490.19641530.15572890X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1138-0.18550.54064.20250.57252.5448-0.027-0.19710.03870.0805-0.09650.0468-0.2536-0.3090.09320.16630.04010.00470.2414-0.01270.147613.0225-31.8435-6.7439
22.60330.16670.79782.6810.42034.8719-0.14070.01160.11940.0780.07260.1423-0.1015-0.2880.08340.21250.0025-0.01130.1768-0.01260.2582-2.922-7.8939-25.9262
30.9894-0.07410.95091.2534-0.39094.4380.00680.1443-0.0214-0.12950.0113-0.0547-0.17780.2331-0.0220.1590.0070.02270.2308-0.00940.209620.1291-36.627-27.7982
40.46440.337-0.17056.54412.41832.4154-0.05880.04490.1229-0.04540.03890.0127-0.09490.08740.01960.22230.0051-0.04050.20630.00640.27610.0809-2.9087-34.9016
53.77334.2138-3.51534.8103-3.96643.29120.2064-0.6985-0.49320.3768-0.384-0.66620.4390.54020.13870.27010.0147-0.01070.31470.01740.260222.8913-44.8578-5.9032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 214 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 107 )
4X-RAY DIFFRACTION4chain 'B' and (resid 108 through 213 )
5X-RAY DIFFRACTION5chain 'C' and (resid 4 through 13 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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