[English] 日本語
Yorodumi
- PDB-6b5o: Structure of PfCSP peptide 29 with human protective antibody CIS43 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b5o
TitleStructure of PfCSP peptide 29 with human protective antibody CIS43
Components
  • CIS43 Fab Heavy chain
  • CIS43 Fab Light chain
  • PfCSP peptide 29: ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN
KeywordsIMMUNE SYSTEM / Malaria / pfCSP / vaccine / antibodies
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium Falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.194 Å
AuthorsPancera, M. / Weidle, C.
CitationJournal: Nat. Med. / Year: 2018
Title: A human monoclonal antibody prevents malaria infection by targeting a new site of vulnerability on the parasite.
Authors: Kisalu, N.K. / Idris, A.H. / Weidle, C. / Flores-Garcia, Y. / Flynn, B.J. / Sack, B.K. / Murphy, S. / Schon, A. / Freire, E. / Francica, J.R. / Miller, A.B. / Gregory, J. / March, S. / Liao, ...Authors: Kisalu, N.K. / Idris, A.H. / Weidle, C. / Flores-Garcia, Y. / Flynn, B.J. / Sack, B.K. / Murphy, S. / Schon, A. / Freire, E. / Francica, J.R. / Miller, A.B. / Gregory, J. / March, S. / Liao, H.X. / Haynes, B.F. / Wiehe, K. / Trama, A.M. / Saunders, K.O. / Gladden, M.A. / Monroe, A. / Bonsignori, M. / Kanekiyo, M. / Wheatley, A.K. / McDermott, A.B. / Farney, S.K. / Chuang, G.Y. / Zhang, B. / Kc, N. / Chakravarty, S. / Kwong, P.D. / Sinnis, P. / Bhatia, S.N. / Kappe, S.H.I. / Sim, B.K.L. / Hoffman, S.L. / Zavala, F. / Pancera, M. / Seder, R.A.
History
DepositionSep 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: CIS43 Fab Heavy chain
L: CIS43 Fab Light chain
A: PfCSP peptide 29: ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN


Theoretical massNumber of molelcules
Total (without water)49,8513
Polymers49,8513
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-30 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.244, 60.410, 84.841
Angle α, β, γ (deg.)90.00, 107.02, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody CIS43 Fab Heavy chain


Mass: 24206.227 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 CIS43 Fab Light chain


Mass: 24138.707 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: Protein/peptide PfCSP peptide 29: ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN


Mass: 1506.493 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium Falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.6M Sodium Citrate Tribasic Dihydrate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 22790 / % possible obs: 98.7 % / Redundancy: 13.5 % / Net I/σ(I): 13.5

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.194→50 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.89
RfactorNum. reflection% reflection
Rfree0.2401 1169 5.13 %
Rwork0.1929 --
obs0.1953 22773 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.194→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 0 124 3546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023505
X-RAY DIFFRACTIONf_angle_d0.6074778
X-RAY DIFFRACTIONf_dihedral_angle_d11.4912105
X-RAY DIFFRACTIONf_chiral_restr0.046543
X-RAY DIFFRACTIONf_plane_restr0.003610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1943-2.29410.32941250.28372303X-RAY DIFFRACTION83
2.2941-2.41510.32041330.26062750X-RAY DIFFRACTION99
2.4151-2.56640.3041600.24412690X-RAY DIFFRACTION100
2.5664-2.76450.31031490.24122762X-RAY DIFFRACTION100
2.7645-3.04270.26121470.23022743X-RAY DIFFRACTION100
3.0427-3.48290.27491520.20762756X-RAY DIFFRACTION100
3.4829-4.38760.19191490.16422762X-RAY DIFFRACTION100
4.3876-50.02440.20431540.15632838X-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)
12.57451.1795-1.31995.8216-0.76683.2728-0.0142-0.1103-0.0375-0.52060.17890.50450.3521-0.3858-0.11630.3511-0.0444-0.07230.47520.03930.4831-43.4878-8.730317.6874
23.17370.0077-0.93023.7244-1.033.6883-0.0069-0.49120.16220.33430.03770.1951-0.2492-0.0855-0.15890.3739-0.03210.02840.5729-0.01240.4622-38.3486-7.316229.9732
34.00720.5911-1.48035.4229-3.38435.59580.3204-0.5880.1887-0.0972-0.18061.078-0.2789-0.5698-0.18730.36060.04060.04650.7-0.00290.6266-47.1141-6.799526.5633
47.5216-2.1956-1.02343.2039-1.10188.07530.34070.01360.42210.1232-0.0724-0.0589-0.65310.065-0.12120.3479-0.0115-0.02460.3718-0.07910.3431-37.86920.135419.2137
50.98740.04760.14050.74740.70332.48140.0316-0.147-0.0826-0.0808-0.05240.14860.0502-0.09280.12860.3386-0.0155-0.03440.33730.01210.44-31.7151-13.79817.0316
61.22780.0632-0.02352.33660.80130.7999-0.07470.0386-0.0475-0.1704-0.00220.2094-0.05960.00770.0650.38040.0039-0.05350.31190.03470.3651-28.8449-16.2466-1.1532
78.8215-4.8323-5.9715.30515.26477.4112-0.15080.44810.0062-0.15-0.04420.3610.2305-0.26690.13610.5019-0.12430.09240.4628-0.03150.5655-35.9555-20.1691-6.5471
82.45910.41370.03731.81340.15813.0973-0.0294-0.3854-0.12790.01160.06320.04710.20830.0637-0.04450.34570.0266-0.02570.53490.02180.32-18.0617-11.952630.1459
91.0376-0.5114-0.48290.68690.31691.5029-0.0636-0.16840.0738-0.07750.04340.11660.08570.0458-0.08830.3728-0.0539-0.01170.301-0.02960.4302-21.5437-10.10017.2518
102.6329-2.13152.33971.8863-1.23015.74440.0482-0.10120.1417-0.17560.05520.1715-0.1954-0.01780.1830.3655-0.055-0.02170.24860.01220.3721-16.0876-7.5555-3.9275
114.3553-1.49024.01262.1956-0.81655.1656-0.01110.65110.3389-0.4355-0.1741-0.01290.13080.2510.15090.5211-0.0403-0.0060.34130.05920.3603-17.5481-7.3969-15.4502
120.0209-0.02760.0240.0309-0.02420.0159-0.8124-0.89730.43470.58850.0579-0.2043-0.4989-0.2377-0.00120.65450.0114-0.01931.0351-0.09590.6158-33.5172-10.607440.7821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 25 )
2X-RAY DIFFRACTION2chain 'H' and (resid 26 through 63 )
3X-RAY DIFFRACTION3chain 'H' and (resid 64 through 82 )
4X-RAY DIFFRACTION4chain 'H' and (resid 83 through 93 )
5X-RAY DIFFRACTION5chain 'H' and (resid 94 through 157 )
6X-RAY DIFFRACTION6chain 'H' and (resid 158 through 203 )
7X-RAY DIFFRACTION7chain 'H' and (resid 204 through 214 )
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 90 )
9X-RAY DIFFRACTION9chain 'L' and (resid 91 through 128 )
10X-RAY DIFFRACTION10chain 'L' and (resid 129 through 174 )
11X-RAY DIFFRACTION11chain 'L' and (resid 175 through 213 )
12X-RAY DIFFRACTION12chain 'A' and (resid 3 through 11 )

+
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