[English] 日本語
Yorodumi
- PDB-6o28: Crystal structure of 4493 Fab in complex with circumsporozoite pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o28
TitleCrystal structure of 4493 Fab in complex with circumsporozoite protein KQPA and anti-kappa VHH domain
Components
  • 4493 Fab heavy chain
  • 4493 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 / external side of 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)
Lama glama (llama)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4493 Fab heavy chain
B: 4493 Kappa light chain
C: 4493 Fab heavy chain
D: 4493 Kappa light chain
E: Circumsporozoite protein
F: Circumsporozoite protein
G: Anti-kappa VHH domain
K: Anti-kappa VHH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,63114
Polymers120,2598
Non-polymers3726
Water16,880937
1
A: 4493 Fab heavy chain
B: 4493 Kappa light chain
E: Circumsporozoite protein
G: Anti-kappa VHH domain


Theoretical massNumber of molelcules
Total (without water)60,1304
Polymers60,1304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 4493 Fab heavy chain
D: 4493 Kappa light chain
F: Circumsporozoite protein
K: Anti-kappa VHH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,50210
Polymers60,1304
Non-polymers3726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.958, 94.676, 143.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 127 or resid 134...
21(chain C and (resid 1 through 139 or resid 141 through 195 or resid 197 through 213))
12chain B
22chain D
13chain E
23chain F
14chain G
24(chain K and ((resid 1 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUSERSER(chain A and (resid 1 through 127 or resid 134...AA1 - 1271 - 136
121GLYGLYGLYGLY(chain A and (resid 1 through 127 or resid 134...AA134 - 139143 - 148
131LEULEULEULEU(chain A and (resid 1 through 127 or resid 134...AA141150
211GLUGLUGLYGLY(chain C and (resid 1 through 139 or resid 141 through 195 or resid 197 through 213))CC1 - 1391 - 148
221LEULEUILEILE(chain C and (resid 1 through 139 or resid 141 through 195 or resid 197 through 213))CC141 - 195150 - 204
231ASNASNPROPRO(chain C and (resid 1 through 139 or resid 141 through 195 or resid 197 through 213))CC197 - 213206 - 222
112GLUGLUGLUGLUchain BBB1 - 2131 - 214
212GLUGLUGLUGLUchain DDD1 - 2131 - 214
113GLYGLYASNASNchain EEE6 - 156 - 15
213GLYGLYASNASNchain FFF6 - 156 - 15
114UNKUNKSERSERchain GGG1 - 1131 - 121
214UNKUNKUNKUNK(chain K and ((resid 1 and (name N or name...KH11
224UNKUNKSERSER(chain K and ((resid 1 and (name N or name...KH1 - 1131 - 121
234UNKUNKSERSER(chain K and ((resid 1 and (name N or name...KH1 - 1131 - 121
244UNKUNKSERSER(chain K and ((resid 1 and (name N or name...KH1 - 1131 - 121
254UNKUNKSERSER(chain K and ((resid 1 and (name N or name...KH1 - 1131 - 121

NCS ensembles :
ID
1
2
3
4

-
Components

-
Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Circumsporozoite protein / / CS


Mass: 1549.577 Da / Num. of mol.: 2 / Fragment: residues 95-109 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P19597

-
Antibody , 3 types, 6 molecules ACBDGK

#1: Antibody 4493 Fab heavy chain


Mass: 23792.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 4493 Kappa light chain


Mass: 23460.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Anti-kappa VHH domain


Mass: 11326.253 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 2 types, 943 molecules

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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 937 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.0, 1 M lithium chloride, 20 % (w/v) PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. obs: 79786 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.054 / Net I/σ(I): 9.4
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3549 / CC1/2: 0.65 / Rpim(I) all: 0.239 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house model

Resolution: 1.93→29.237 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 1530 1.92 %
Rwork0.1881 78035 -
obs0.1887 79565 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.02 Å2 / Biso mean: 30.3621 Å2 / Biso min: 12.26 Å2
Refinement stepCycle: final / Resolution: 1.93→29.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8075 0 24 937 9036
Biso mean--55.74 37.72 -
Num. residues----1120
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1954X-RAY DIFFRACTION6.495TORSIONAL
12C1954X-RAY DIFFRACTION6.495TORSIONAL
21B2044X-RAY DIFFRACTION6.495TORSIONAL
22D2044X-RAY DIFFRACTION6.495TORSIONAL
31E92X-RAY DIFFRACTION6.495TORSIONAL
32F92X-RAY DIFFRACTION6.495TORSIONAL
41G1058X-RAY DIFFRACTION6.495TORSIONAL
42K1058X-RAY DIFFRACTION6.495TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.93-1.99230.30551370.26326990100
1.9923-2.06350.23811380.23697021100
2.0635-2.14610.2741370.22557017100
2.1461-2.24370.27241380.23367011100
2.2437-2.36190.25961380.23427042100
2.3619-2.50990.27541370.21557050100
2.5099-2.70350.25491400.20027081100
2.7035-2.97530.2191380.18997125100
2.9753-3.40530.21881400.1747123100
3.4053-4.28820.15061410.15147198100
4.2882-29.2370.19841460.1609737799
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)
12.8503-0.55360.99470.7227-0.66611.1035-0.09710.076-0.09030.08080.03690.0383-0.0497-0.00720.07250.20380.00290.01150.1980.01990.2396-49.18562.5827.0077
22.74560.1724-2.49980.5295-0.12434.9625-0.09690.0507-0.1205-0.1530.001-0.02150.2181-0.03780.11240.2627-0.01490.01750.1766-0.01310.2315-55.79219.6674-26.6773
31.02090.10210.73141.356-0.60013.5587-0.02050.13660.1012-0.0777-0.0249-0.17440.03160.24950.04220.2373-0.0324-0.01470.27940.02280.2973-33.556317.9022.2619
45.61421.43010.82421.5654-0.03721.4546-0.13780.04630.2191-0.04360.10370.2735-0.0586-0.17830.03860.2329-0.01980.01120.225-0.01140.217-54.949126.0068-26.0968
52.44610.5763-0.58851.0348-0.5051.3172-0.0691-0.06510.0525-0.05780.04230.07050.0268-0.05060.02410.21360.0012-0.01320.20470.01040.2-10.8123-2.403-6.4149
63.9286-0.21772.0821.04280.26354.2577-0.1205-0.24550.18550.15360.0313-0.0725-0.1269-0.05460.08720.20850.0102-0.02860.1683-0.01820.2421-17.4177-10.389826.7965
71.1879-0.3618-0.1641.7452-0.51132.8971-0.0147-0.0003-0.06780.0461-0.043-0.10860.0870.1570.06760.18750.01330.0080.18760.01010.21864.8193-17.7547-1.6733
84.47670.202-0.81960.8298-0.39691.3667-0.0713-0.1771-0.0798-0.02410.05580.10680.0454-0.06770.00770.21460.0209-0.02460.19560.0050.1812-16.6622-26.955625.8125
96.5798-1.46233.03524.0238-5.36547.6686-0.0468-1.59990.24381.0732-0.02720.38160.0918-0.4403-0.04520.5058-0.01040.04980.4684-0.0580.2618-42.06465.380122.7139
107.75930.496-1.70533.9264-4.82126.2874-0.36121.2866-0.1817-0.76640.18080.4730.187-0.37980.07030.4542-0.04080.01450.3783-0.0270.2225-3.6618-5.1205-22.1524
113.1825-0.3327-1.68741.18220.18872.53180.01270.04830.0064-0.0249-0.0376-0.0656-0.0814-0.07490.00960.1671-0.0186-0.00870.1402-0.01040.1719-31.308442.2274-21.805
121.70530.23940.99541.3506-0.25742.42990.01660.0468-0.0956-0.0562-0.0023-0.04570.0513-0.0402-0.01020.20070.0320.01780.18620.00410.23086.9014-43.116721.9347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )A1 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 213 )A114 - 213
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 107 )B1 - 107
4X-RAY DIFFRACTION4chain 'B' and (resid 108 through 213 )B108 - 213
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 113 )C1 - 113
6X-RAY DIFFRACTION6chain 'C' and (resid 114 through 213 )C114 - 213
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 107 )D1 - 107
8X-RAY DIFFRACTION8chain 'D' and (resid 108 through 213 )D108 - 213
9X-RAY DIFFRACTION9chain 'E' and (resid 6 through 15 )E6 - 15
10X-RAY DIFFRACTION10chain 'F' and (resid 6 through 15 )F6 - 15
11X-RAY DIFFRACTION11chain 'G' and (resid 1 through 113 )G1 - 113
12X-RAY DIFFRACTION12chain 'K' and (resid 1 through 113 )K1 - 113

+
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