[English] 日本語
Yorodumi
- PDB-6d0x: Crystal structure of chimeric H.2140 / K.1210 Fab in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d0x
TitleCrystal structure of chimeric H.2140 / K.1210 Fab in complex with circumsporozoite protein NANP3
Components
  • 1210 Antibody, light chain
  • 2140 Antibody, heavy chain
  • NANP3
KeywordsIMMUNE SYSTEM / Malaria / Antibody / Circumsporozoite protein
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
DI(HYDROXYETHYL)ETHER / Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsScally, S.W. / Bosch, A. / Imkeller, K. / Wardemann, H. / Julien, J.P.
CitationJournal: Science / Year: 2018
Title: Antihomotypic affinity maturation improves human B cell responses against a repetitive epitope.
Authors: Imkeller, K. / Scally, S.W. / Bosch, A. / Marti, G.P. / Costa, G. / Triller, G. / Murugan, R. / Renna, V. / Jumaa, H. / Kremsner, P.G. / Sim, B.K.L. / Hoffman, S.L. / Mordmuller, B. / ...Authors: Imkeller, K. / Scally, S.W. / Bosch, A. / Marti, G.P. / Costa, G. / Triller, G. / Murugan, R. / Renna, V. / Jumaa, H. / Kremsner, P.G. / Sim, B.K.L. / Hoffman, S.L. / Mordmuller, B. / Levashina, E.A. / Julien, J.P. / Wardemann, H.
History
DepositionApr 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 4, 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
A: 2140 Antibody, heavy chain
B: 1210 Antibody, light chain
C: NANP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2617
Polymers48,8783
Non-polymers3824
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-30 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.113, 83.113, 157.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-443-

HOH

21B-503-

HOH

-
Components

-
Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide NANP3


Mass: 1207.210 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS

-
Antibody , 2 types, 2 molecules AB

#1: Antibody 2140 Antibody, heavy chain


Mass: 24173.002 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 1210 Antibody, light chain


Mass: 23498.098 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 , 3 types, 273 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH 6.5, 20% (w/v) PEG4000, 0.6M NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03327 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03327 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 47923 / % possible obs: 99.7 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.02 / Net I/σ(I): 21.8
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6923 / CC1/2: 0.766 / Rpim(I) all: 0.223 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.849→39.291 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 1999 4.18 %
Rwork0.179 --
obs0.1803 47836 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.849→39.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 0 25 269 3623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133472
X-RAY DIFFRACTIONf_angle_d1.2114744
X-RAY DIFFRACTIONf_dihedral_angle_d14.0242056
X-RAY DIFFRACTIONf_chiral_restr0.082532
X-RAY DIFFRACTIONf_plane_restr0.009611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8486-1.89490.3241390.3083183X-RAY DIFFRACTION99
1.8949-1.94610.32241400.26773198X-RAY DIFFRACTION100
1.9461-2.00340.2741400.23383222X-RAY DIFFRACTION100
2.0034-2.0680.25551410.21453248X-RAY DIFFRACTION100
2.068-2.14190.22821420.20713232X-RAY DIFFRACTION100
2.1419-2.22770.23971410.19763222X-RAY DIFFRACTION100
2.2277-2.3290.25921400.19843228X-RAY DIFFRACTION100
2.329-2.45180.25981430.2093285X-RAY DIFFRACTION100
2.4518-2.60540.28711420.20453239X-RAY DIFFRACTION100
2.6054-2.80650.22141430.20213282X-RAY DIFFRACTION100
2.8065-3.08890.20941440.1973298X-RAY DIFFRACTION100
3.0889-3.53560.19251430.17773297X-RAY DIFFRACTION100
3.5356-4.45350.17031480.14693359X-RAY DIFFRACTION100
4.4535-39.30040.18631530.15313544X-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)
12.1568-0.9282-1.25891.51081.2823.38170.01640.12750.0555-0.04740.0189-0.1866-0.12260.2681-0.04940.1755-0.03170.00050.2774-0.0030.2838361.9344-99.209520.4194
23.11211.85622.1784.77160.59472.04740.39291.1575-0.811-1.1715-0.08961.1323-0.1802-1.0892-0.40550.59580.2249-0.20211.5323-0.33280.7612345.3726-110.2783-16.2008
35.1452-0.25122.51623.05841.20942.9776-0.01391.27750.1495-0.631-0.18630.2639-0.3638-0.79570.17670.4150.1125-0.01461.0242-0.07830.4303353.5237-105.4904-11.9142
44.6853-3.46063.72648.78-7.32279.53650.24280.26180.067-0.1767-0.23840.36050.2317-0.3343-0.02760.2104-0.01930.02320.4449-0.10820.3209336.8899-97.208318.3898
53.2275-0.96091.45372.0002-0.96644.6693-0.00640.2210.2793-0.0339-0.1294-0.0471-0.2966-0.19870.12080.19820.00150.00820.2247-0.03310.2911342.7086-90.844521.8878
61.82911.55142.71.34582.3594.018-0.03361.212-0.9074-0.2821-0.6570.8619-0.2652-0.62170.59060.34050.2034-0.04571.0786-0.33680.7251333.5115-97.1212.134
75.84740.78521.56741.1097-0.31132.4991-0.47011.1191-0.9228-0.30290.0018-0.26190.14770.13920.13670.4280.0806-0.13421.4727-0.75050.879347.3466-118.023-14.4188
84.8647-1.86-0.38055.65412.57295.63940.01270.6763-0.39420.4408-0.56720.640.3581-1.15750.55960.48280.0133-0.03981.1894-0.47210.7996338.4827-111.8788-4.662
92.89752.97292.56914.00490.73246.29540.51210.4409-1.19690.1428-0.54450.95720.9982-1.1870.05930.5362-0.13360.04270.9885-0.41111.0906340.7584-120.8659-1.7303
103.93830.41481.266.30142.86285.41260.10550.8005-0.9682-0.0641-0.31140.52950.3415-0.73120.21760.39140.0337-0.00780.9665-0.35540.7459341.5453-114.8095-6.4522
113.3941-2.7141-3.99856.95034.7677.04240.16560.4971-0.24420.164-0.10470.68770.380.225-0.06060.51350.0024-0.02841.6531-0.69131.0943331.9665-115.7467-10.1043
123.6548-3.00440.37017.6485-7.45672.03450.652-0.15210.09271.0156-0.26190.0144-0.64120.4668-0.4380.3831-0.09950.01490.3647-0.08380.361357.2901-93.337538.3101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 124 )
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 145 )
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 213 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 18 )
5X-RAY DIFFRACTION5chain 'B' and (resid 19 through 101 )
6X-RAY DIFFRACTION6chain 'B' and (resid 102 through 113 )
7X-RAY DIFFRACTION7chain 'B' and (resid 114 through 128 )
8X-RAY DIFFRACTION8chain 'B' and (resid 129 through 150 )
9X-RAY DIFFRACTION9chain 'B' and (resid 151 through 163 )
10X-RAY DIFFRACTION10chain 'B' and (resid 164 through 197 )
11X-RAY DIFFRACTION11chain 'B' and (resid 198 through 212 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 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