[English] 日本語
Yorodumi
- PDB-6b0e: Crystal structure of Pfs25 in complex with the transmission block... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b0e
TitleCrystal structure of Pfs25 in complex with the transmission blocking antibody 1260
Components
  • 1260 antibody, heavy chain
  • 1260 antibody, light chain
  • 25 kDa ookinete surface antigen
KeywordsIMMUNE SYSTEM / Transmission blocking vaccine / malaria / antibody / EGF-like domain
Function / homology
Function and homology information


side of membrane / cell surface / plasma membrane
Similarity search - Function
Plasmodium vivax P25 fold / Plasmodium vivax P25 domain / Ookinete surface antigen, EGF domain / Pvs28 EGF domain / Orthogonal Prism / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulins / Immunoglobulin-like ...Plasmodium vivax P25 fold / Plasmodium vivax P25 domain / Ookinete surface antigen, EGF domain / Pvs28 EGF domain / Orthogonal Prism / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
25 kDa ookinete surface antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsScally, S.W. / McLeod, B. / Bosch, A. / King, C.R. / Julien, J.P.
CitationJournal: Nat Commun / Year: 2017
Title: Molecular definition of multiple sites of antibody inhibition of malaria transmission-blocking vaccine antigen Pfs25.
Authors: Scally, S.W. / McLeod, B. / Bosch, A. / Miura, K. / Liang, Q. / Carroll, S. / Reponen, S. / Nguyen, N. / Giladi, E. / Ramisch, S. / Yusibov, V. / Bradley, A. / Lemiale, F. / Schief, W.R. / ...Authors: Scally, S.W. / McLeod, B. / Bosch, A. / Miura, K. / Liang, Q. / Carroll, S. / Reponen, S. / Nguyen, N. / Giladi, E. / Ramisch, S. / Yusibov, V. / Bradley, A. / Lemiale, F. / Schief, W.R. / Emerling, D. / Kellam, P. / King, C.R. / Julien, J.P.
History
DepositionSep 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Oct 4, 2023Group: 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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 1260 antibody, light chain
B: 1260 antibody, heavy chain
E: 25 kDa ookinete surface antigen


Theoretical massNumber of molelcules
Total (without water)68,6523
Polymers68,6523
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-22 kcal/mol
Surface area28200 Å2
Unit cell
Length a, b, c (Å)53.223, 79.635, 78.065
Angle α, β, γ (deg.)90.00, 90.91, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody 1260 antibody, light chain


Mass: 23980.666 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 1260 antibody, heavy chain


Mass: 24567.396 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 25 kDa ookinete surface antigen / Pfs25


Mass: 20104.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Homo sapiens (human) / References: UniProt: P13829
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.0 M ammonium sulfate, 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. obs: 9915 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rpim(I) all: 0.044 / Net I/σ(I): 14.6
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 835 / Rpim(I) all: 0.362 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XPREPdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z27, 5D1X

1z27

5d1x


Resolution: 3.3→39.818 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.53
RfactorNum. reflection% reflection
Rfree0.2802 497 5.02 %
Rwork0.2304 --
obs0.233 9909 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→39.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 0 0 4204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024300
X-RAY DIFFRACTIONf_angle_d0.4765890
X-RAY DIFFRACTIONf_dihedral_angle_d8.8472556
X-RAY DIFFRACTIONf_chiral_restr0.04690
X-RAY DIFFRACTIONf_plane_restr0.003761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.6320.37111160.31862337X-RAY DIFFRACTION100
3.632-4.1570.34431270.27492347X-RAY DIFFRACTION100
4.157-5.23560.23491300.2142338X-RAY DIFFRACTION100
5.2356-39.82040.26931240.20582390X-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)
15.79452.75714.26898.16122.57799.22010.79161.0606-1.3135-1.63320.8046-0.13021.49151.2635-0.87451.435-0.1045-0.29230.7441-0.07111.3535-16.3983-13.3676-39.7872
27.4556-5.63115.22888.1728-2.60228.23520.34480.6716-0.1232-0.6923-0.0979-0.35890.32690.752-0.22650.7907-0.08360.07680.805-0.15960.9863-12.5274-6.901-36.3572
36.8145-4.1409-5.7836.498-1.54922.07862.7595-0.9741-1.4234-0.1036-0.6217-0.4974-3.81130.2402-0.40972.44150.3136-0.92852.2913-0.45551.3543-6.1996-15.12834.6192
47.3543-3.6319-0.44656.10540.062810.00890.3732-0.51380.11890.66620.8187-0.57742.04481.3573-0.88131.38310.439-0.50931.0024-0.40391.035-5.4045-19.4276-9.2085
56.91933.3811-2.45325.55892.21036.74041.0633-0.6803-0.44241.74110.1144-0.3102-0.8532-0.166-0.86141.3520.2523-0.67721.2758-0.21351.755-6.7916-16.4382-11.808
64.1815-1.70541.09938.594-1.67194.14050.2959-1.2953-0.89281.73951.1194-0.36341.4530.3356-0.78651.82590.4803-0.62961.43790.01181.385-6.3686-24.2539-0.9881
77.7457-2.6234-1.81019.5938-6.60216.4481-0.1687-2.79850.34011.8854-0.134-0.7998-2.42740.58140.14051.20530.0712-0.10671.4716-0.06981.249-26.97475.6301-19.8408
82.4728-2.34071.43184.4127-0.88833.3931-1.1677-1.1689-0.49592.10911.94921.4481-2.6783-0.7312-0.73540.94610.24130.22070.97530.11480.8691-28.88046.0938-30.2194
93.2209-2.0757-2.35194.5914-0.1687.4155-0.52820.8206-1.1394-0.18270.78871.18180.7317-1.125-1.35850.8146-0.1072-0.00311.10180.45241.7547-33.2129-3.7175-30.4778
106.9794-1.57381.1777.5857-5.00634.3682-0.484-1.33070.71351.1826-0.1847-1.4401-1.9235-2.19040.21191.16540.54310.40211.42470.20441.0413-36.11695.8002-26.0064
114.19480.34441.95112.76171.56934.4167-0.2926-1.1431-1.37592.30881.8381.0670.5199-0.223-0.32711.08690.23210.70420.97490.3091.3065-28.2704-2.9356-22.0457
123.8785-2.47051.80045.7331-4.80656.7455-0.6751-1.14720.02751.06831.3345-0.0076-1.3888-0.5605-0.49511.11440.1642-0.03370.8226-0.21271.036-18.5999-2.8413-18.0239
131.9385-2.9086-1.33617.6514.3392.6526-0.5089-0.7631.12081.81092.4465-1.7714-1.2544-1.28870.11572.50730.4031-0.74621.8398-0.11811.2625-3.2693-0.2171-6.058
146.67620.2125-3.79342.0243-2.98723.05351.288-3.75721.89492.8936-0.6674-2.1598-0.7372-1.81560.14541.3170.6158-0.09242.0697-0.24220.9773-10.0694-8.7252-5.3944
153.0393-0.1524-3.42378.0995-6.31769.4672-1.1778-1.42513.23820.6903-1.0369-2.6309-2.35661.53561.42121.3609-0.3516-0.69342.5649-0.50151.85067.2845-4.34442.9259
162.0163-5.33025.1367.4261-8.29059.223-0.759-1.12762.92012.60541.9616-2.5811-2.63740.90290.29232.58520.53630.01321.6529-0.7691.4166-6.69380.99063.1653
177.50520.9581-2.09728.18820.66830.74531.10490.85481.46-2.8169-1.04992.40271.849-1.26590.8511.8659-0.4659-0.54210.8537-0.01251.3187-35.02268.0553-59.3379
186.1928-6.7232-6.44048.25817.49447.32490.53610.5479-2.0148-0.1091-1.10622.01811.3215-0.52320.98092.5346-0.1139-0.59241.2641-0.17061.9343-32.8403-10.2595-64.8994
192.29020.0971.13912.4382-1.77952.7321.9959-0.8580.8395-1.8793-0.01992.92233.05591.3777-1.55692.57420.072-0.03651.4296-0.18411.2381-20.2175-3.9638-62.0742
204.18130.85093.84552.0072-6.27288.45521.54230.4423-0.5752-3.53930.348-1.26561.02333.51131.15131.7654-0.09150.75141.25020.43031.2656-18.5177.6595-60.1756
213.2556-4.4751.63387.8728-0.99186.9718-1.0690.2830.6826-0.22861.01760.34340.0601-0.4814-0.11311.0389-0.2652-0.19990.81920.26660.9197-33.283612.6679-50.02
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 113 )
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 174 )
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 212 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 17 )
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 40 )
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 63 )
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 82 )
11X-RAY DIFFRACTION11chain 'B' and (resid 82A through 95 )
12X-RAY DIFFRACTION12chain 'B' and (resid 96 through 145 )
13X-RAY DIFFRACTION13chain 'B' and (resid 146 through 165 )
14X-RAY DIFFRACTION14chain 'B' and (resid 166 through 185 )
15X-RAY DIFFRACTION15chain 'B' and (resid 186 through 197 )
16X-RAY DIFFRACTION16chain 'B' and (resid 198 through 211 )
17X-RAY DIFFRACTION17chain 'E' and (resid 2 through 25 )
18X-RAY DIFFRACTION18chain 'E' and (resid 26 through 76 )
19X-RAY DIFFRACTION19chain 'E' and (resid 77 through 89 )
20X-RAY DIFFRACTION20chain 'E' and (resid 90 through 109 )
21X-RAY DIFFRACTION21chain 'E' and (resid 110 through 172 )

+
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