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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ulf
TitleCrystal structure of 4498 Fab in complex with circumsporozoite protein NDN3 and anti-Kappa VHH domain
Components
  • 4498 Fab heavy chain
  • 4498 Fab light chain
  • Circumsporozoite protein
  • anti Kappa VHH domain
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
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Camelidae mixed library (mammal)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsThai, E. / Scally, S.W. / Prieto, K. / Murugan, R. / Wardemann, H. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1179906; J.-P.J. United States
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
DepositionOct 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 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 1.3Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4498 Fab heavy chain
B: 4498 Fab light chain
K: anti Kappa VHH domain
P: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)60,6844
Polymers60,6844
Non-polymers00
Water11,440635
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-37 kcal/mol
Surface area25020 Å2
Unit cell
Length a, b, c (Å)61.536, 76.084, 63.247
Angle α, β, γ (deg.)90.000, 98.321, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Antibody 4498 Fab heavy chain


Mass: 24749.605 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 Fab 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: obtained synthetically / Source: (synth.) Camelidae mixed library (mammal)
#4: Protein/peptide Circumsporozoite protein / / CS


Mass: 1236.248 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M phosphate-citrate pH 4.2, 20 % (w/v) PEG 8000, 0.2 M sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 62305 / % possible obs: 98.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.85 Å2 / CC1/2: 0.999 / Net I/σ(I): 26.5
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 3120 / CC1/2: 0.978

-
Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D01
Resolution: 1.7→38.04 Å / SU ML: 0.1804 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.6205
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2351 2003 3.22 %
Rwork0.2074 60263 -
obs0.2083 62266 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 0 635 4799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00574264
X-RAY DIFFRACTIONf_angle_d0.87285824
X-RAY DIFFRACTIONf_chiral_restr0.0604663
X-RAY DIFFRACTIONf_plane_restr0.0055757
X-RAY DIFFRACTIONf_dihedral_angle_d16.52841444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.31611450.25914223X-RAY DIFFRACTION96.72
1.74-1.790.2281330.24594214X-RAY DIFFRACTION96.82
1.79-1.840.29771410.23444255X-RAY DIFFRACTION97.21
1.84-1.90.30731390.22714268X-RAY DIFFRACTION97.44
1.9-1.970.23671430.20984240X-RAY DIFFRACTION97.4
1.97-2.050.24531380.21074300X-RAY DIFFRACTION97.69
2.05-2.140.2361420.20484278X-RAY DIFFRACTION97.92
2.14-2.250.23161450.20494312X-RAY DIFFRACTION98.19
2.25-2.40.22291480.21214287X-RAY DIFFRACTION98.45
2.4-2.580.24481440.21924352X-RAY DIFFRACTION98.68
2.58-2.840.23911420.21124331X-RAY DIFFRACTION98.81
2.84-3.250.22891440.20244370X-RAY DIFFRACTION98.93
3.25-4.090.1881470.18834370X-RAY DIFFRACTION99.01
4.1-38.040.25051520.20224463X-RAY DIFFRACTION99.53
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9086806917420.08512184462680.2920028742761.72862520002-0.2175496264222.88784197382-0.02235195690360.02143852761550.07419071717770.0849277935761-0.007023202038530.00451431519587-0.09282174439440.04811135284760.0174931791610.07905509650970.0004642212380850.004682359197460.1022971463870.009525451341920.0897213543583-27.3281950691-15.1070480182-15.0739324354
27.700269146990.29754394766-1.651906441943.87295258712-3.234936198429.30752630828-0.06833062818740.157103460481-0.52571799301-0.0134570847018-0.127988457047-1.700458872480.5608980778180.7082229537050.1775312314520.2232272403970.12547796395-0.008938772840630.3856481959390.01139449276370.37087768564312.3895394589-6.65420483883-12.7723031778
32.62055335836-0.6803547412480.07700477266852.876503315850.05182056515023.02486342781-0.00308570627418-0.0136879522299-0.00989081918840.0443017432478-0.00729050925341-0.2367241165960.07820993240370.2947352208440.00856579303020.1039665565490.0187528269923-0.01666241590730.1436116743270.001242063051270.148849986236-0.131121122672-0.57091387074-6.20794083602
43.542402806360.488156823280.6703354581731.315641866380.8186862395372.79139281245-0.1486621365760.0435295777768-0.003161830310940.06335581814540.05681431022240.1065323494670.18844312257-0.1198547799240.0852842799770.2382168123560.02047607468060.04469849316270.1149999120370.02430861441320.114924326185-32.481934299618.1595699713-7.78108440642
53.47308687734-0.1778478802091.710129001631.47907626595-0.05427802629122.644189478690.03547957624410.381841966980.119853450649-0.198612918246-0.100215486914-0.2248762691560.01976981040670.5062974823020.06694904798770.1597645020020.03377074407290.03178770042480.210930702810.03929459820520.153434935726-4.414774723762.05362669982-26.9674940669
60.843607870397-0.885373153447-0.3017191153733.286719548391.937247526823.75475447785-0.0800429832681-0.09809326885420.06836520073920.3157017404090.0790966637002-0.048006178247-0.1304905183350.1168901822730.0004014787611560.137932466732-0.023320905898-0.001813886073360.117501273620.008070924596360.107443834361-27.284850569828.1315727728-18.6784641832
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain KKC1 - 1211 - 123
22chain PPD2 - 121 - 11
33chain 'A' and (resid 1 through 127)AA1 - 1271 - 127
44chain 'A' and (resid 128 through 228)AA128 - 228128 - 228
55chain 'B' and (resid 1 through 106)BB1 - 1061 - 106
66chain 'B' and (resid 107 through 213)BB107 - 213107 - 215

+
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