[English] 日本語
Yorodumi
- PDB-6o24: Crystal structure of 4498 Fab in complex with circumsporozoite pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o24
TitleCrystal structure of 4498 Fab in complex with circumsporozoite protein NANP3 and anti-Kappa VHH domain
Components
  • 4498 Fab heavy chain
  • 4498 Kappa light chain
  • Anti-kappa VHH domain
  • Circumsporozoite protein
KeywordsIMMUNE SYSTEM / Malaria / antibody
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / side of membrane / cell surface / 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
Similarity search - Domain/homology
CITRIC ACID / Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsScally, S.W. / Bosch, A. / Prieto, 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 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4498 Fab heavy chain
B: 4498 Kappa light chain
K: Anti-kappa VHH domain
I: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1069
Polymers60,6664
Non-polymers4405
Water12,160675
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-24 kcal/mol
Surface area25100 Å2
Unit cell
Length a, b, c (Å)62.998, 76.785, 63.657
Angle α, β, γ (deg.)90.000, 98.940, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein/peptide , 1 types, 1 molecules I

#4: Protein/peptide Circumsporozoite protein / CS


Mass: 1207.210 Da / Num. of mol.: 1 / Fragment: residues 148-159 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893

-
Antibody , 3 types, 3 molecules ABK

#1: Antibody 4498 Fab heavy chain


Mass: 24760.590 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 4498 Kappa light chain


Mass: 23371.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Anti-kappa VHH domain


Mass: 11326.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 3 types, 680 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 2.5
Details: 10 % (w/v) 2-methyl-2,4-pentanediol, 0.1 M citric acid pH 2.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979341 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979341 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. obs: 117560 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 16.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Net I/σ(I): 12.7
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4896 / CC1/2: 0.791 / Rpim(I) all: 0.26 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Internal Fab model

Resolution: 1.4→19.968 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1862 2010 1.71 %
Rwork0.1612 115474 -
obs0.1616 117484 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.49 Å2 / Biso mean: 28.3645 Å2 / Biso min: 12.35 Å2
Refinement stepCycle: final / Resolution: 1.4→19.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4179 0 29 675 4883
Biso mean--67.74 39.16 -
Num. residues----575
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4-1.4350.29671450.26648182
1.435-1.47380.30081390.24588220
1.4738-1.51720.27281390.2298215
1.5172-1.56610.22461450.20338226
1.5661-1.62210.23961450.1898247
1.6221-1.6870.20551430.18278236
1.687-1.76370.2021430.17188212
1.7637-1.85660.19231480.16818242
1.8566-1.97290.17311450.16038272
1.9729-2.1250.18961410.16278252
2.125-2.33860.19741460.16848223
2.3386-2.67630.18611430.17218264
2.6763-3.36920.19881430.1568281
3.3692-19.9680.14521450.13068402
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)
11.28390.79440.23532.9125-0.96321.36610.0981-0.0176-0.0556-0.153-0.04340.22110.1306-0.0913-0.04640.1808-0.0026-0.07040.1459-0.01040.22390.5819-7.99636.0085
22.60350.10880.63381.4293-0.04523.1425-0.1258-0.06660.01670.04910.0523-0.11880.04340.27520.05680.13790.00910.00610.1388-0.00160.098433.109811.03897.8977
32.59180.2021.46961.1961-0.08192.00220.0425-0.23350.06690.0832-0.04690.25060.0676-0.2779-0.00380.1371-0.0230.01110.1766-0.02340.17394.6166-5.446727.0047
40.49560.5835-0.19372.5952-1.79882.9175-0.02680.0330.034-0.1470.00440.0145-0.11930.03160.02840.14850.016200.1487-0.00150.116927.685620.797218.6975
51.0396-0.27560.50351.3056-0.40552.3972-0.03920.00360.08210.0751-0.0050.0081-0.1665-0.03910.04580.13440.00560.00610.15980.01140.123823.954515.934146.9621
64.3684-1.006-1.15922.3434.64889.4012-0.031-0.1273-0.5640.2076-0.06051.35240.558-0.5040.00210.2416-0.0906-0.08320.273-0.03760.5231-12.1286-14.802512.5576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 113 )A2 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 216 )A114 - 216
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 107 )B1 - 107
4X-RAY DIFFRACTION4chain 'B' and (resid 108 through 214 )B108 - 214
5X-RAY DIFFRACTION5chain 'K' and (resid 1 through 113 )K1 - 113
6X-RAY DIFFRACTION6chain 'I' and (resid 2 through 12 )I2 - 12

+
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