[English] 日本語
Yorodumi
- PDB-8fan: Crystal structure of Ky15.1 Fab in complex with circumsporozoite ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fan
TitleCrystal structure of Ky15.1 Fab in complex with circumsporozoite protein KQPA peptide
Components
  • Circumsporozoite protein KQPA peptide
  • Ky15.1 Antibody, heavy chain
  • Ky15.1 Antibody, light chain
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 speciesMus musculus (house mouse)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBurn Aschner, C. / Thai, E. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1179906 United States
CitationJournal: Cell Rep / Year: 2023
Title: Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein.
Authors: Thai, E. / Murugan, R. / Binter, S. / Burn Aschner, C. / Prieto, K. / Kassardjian, A. / Obraztsova, A.S. / Kang, R.W. / Flores-Garcia, Y. / Mathis-Torres, S. / Li, K. / Horn, G.Q. / ...Authors: Thai, E. / Murugan, R. / Binter, S. / Burn Aschner, C. / Prieto, K. / Kassardjian, A. / Obraztsova, A.S. / Kang, R.W. / Flores-Garcia, Y. / Mathis-Torres, S. / Li, K. / Horn, G.Q. / Huntwork, R.H.C. / Bolscher, J.M. / de Bruijni, M.H.C. / Sauerwein, R. / Dennison, S.M. / Tomaras, G.D. / Zavala, F. / Kellam, P. / Wardemann, H. / Julien, J.P.
History
DepositionNov 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Ky15.1 Antibody, light chain
D: Ky15.1 Antibody, light chain
F: Ky15.1 Antibody, light chain
A: Ky15.1 Antibody, heavy chain
C: Ky15.1 Antibody, heavy chain
E: Ky15.1 Antibody, heavy chain
P: Circumsporozoite protein KQPA peptide
Q: Circumsporozoite protein KQPA peptide
R: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)147,6539
Polymers147,6539
Non-polymers00
Water00
1
D: Ky15.1 Antibody, light chain
C: Ky15.1 Antibody, heavy chain
Q: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)49,2183
Polymers49,2183
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Ky15.1 Antibody, light chain
E: Ky15.1 Antibody, heavy chain
R: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)49,2183
Polymers49,2183
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Ky15.1 Antibody, light chain
A: Ky15.1 Antibody, heavy chain
P: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)49,2183
Polymers49,2183
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-28 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.681, 181.681, 202.648
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

-
Components

#1: Antibody Ky15.1 Antibody, light chain


Mass: 23467.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Ky15.1 Antibody, heavy chain


Mass: 24201.057 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide Circumsporozoite protein KQPA peptide / CS / PfCSP


Mass: 1549.577 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote)
References: UniProt: P19597
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.4 M ammonium sulfate, 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 43443 / % possible obs: 98.1 % / Redundancy: 10 % / Biso Wilson estimate: 47.16 Å2 / CC1/2: 0.98 / Net I/σ(I): 7.7
Reflection shellResolution: 2.9→2.95 Å / Num. unique obs: 2146 / CC1/2: 0.655

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U6V

4u6v


Resolution: 2.9→39.34 Å / SU ML: 0.402 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1403
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2501 1999 4.6 %
Rwork0.2154 41438 -
obs0.217 43437 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.4 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9902 0 0 0 9902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002210139
X-RAY DIFFRACTIONf_angle_d0.546113798
X-RAY DIFFRACTIONf_chiral_restr0.04271549
X-RAY DIFFRACTIONf_plane_restr0.00491766
X-RAY DIFFRACTIONf_dihedral_angle_d11.14423582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.39051410.31112921X-RAY DIFFRACTION99.13
2.97-3.050.33811410.29222918X-RAY DIFFRACTION99
3.05-3.140.35081410.29212934X-RAY DIFFRACTION98.97
3.14-3.240.31971430.28082950X-RAY DIFFRACTION98.94
3.24-3.360.31271410.25892927X-RAY DIFFRACTION98.74
3.36-3.490.27871410.23622938X-RAY DIFFRACTION98.59
3.49-3.650.26631400.22242921X-RAY DIFFRACTION98.84
3.65-3.850.2711430.21212948X-RAY DIFFRACTION98.44
3.85-4.090.23351410.20242932X-RAY DIFFRACTION98.15
4.09-4.40.21431440.17142967X-RAY DIFFRACTION98.14
4.4-4.840.17021430.1582965X-RAY DIFFRACTION98.01
4.84-5.540.19611440.16942975X-RAY DIFFRACTION97.65
5.54-6.980.24481440.22433009X-RAY DIFFRACTION96.9
6.98-39.340.2341520.21333133X-RAY DIFFRACTION95.94
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)
15.925627002121.14104694542-0.8997002998293.38678605512-0.9025455410664.85794518501-0.351372078429-0.802644965647-0.7165762085090.2465408047920.181284216639-0.1787986435060.7134431258670.3212638828480.1662705483420.54188342410.1053757945370.06314872351270.6503114865440.19561585170.75217477239228.38-23.453-18.773
26.18977730661-0.3202112847750.0887401085232.79936437679-1.10639619973.02584265095-0.0116430640784-0.2251087136030.773902591583-0.0680897439101-0.0589342696920.245039086469-0.3432432447580.3136401944170.04000538100110.4624934388550.0470829061006-0.02337633504520.569500645408-0.09089631905170.5445094834345.9793.945-34.872
33.654275882860.3273056784470.1426328999682.72874830463-1.172015795542.13939902902-0.0515735970832-0.04795024346030.0399157032322-0.1765675653080.1310204799120.373445053580.037171023046-0.147091597592-0.09125751971990.3399684291350.0131755975819-0.02843896461960.249723477918-0.02119491549210.23739386348487.172-16.3852.328
43.1146584603-1.380243847661.348261509093.15025786475-1.492957516452.536863709810.2790154895760.0868293391945-0.07039456453830.257177054133-0.624460077004-1.640897471290.1967779939010.6944229294320.2186311102790.4709834468920.00500583494269-0.05222723933130.4365644322360.0732400581761.06482083641120.055-17.16117.132
52.536651109531.997988688950.2170915053953.71436965901-1.383270136231.127024986180.190052134903-0.330738782890.1921311088430.296061031828-0.1081771546430.378836985334-0.272387781522-0.0117450748116-0.06235746849420.366253322638-0.06038479851730.1451315048420.350152484969-0.05745515659730.32277150039355.973-56.172-11.783
64.24898645932-1.80166692442-1.723493832423.655799180761.253031622591.94956617368-0.070337494739-0.121598640744-0.1909219728070.2390396770410.0579183030722-0.1973444659770.505570012064-0.02809577974140.03152354002760.384830266978-0.0356551513361-0.002064434492810.2627696246350.009695351213870.19695442637561.752-88.321-28.82
72.493945810740.039391529399-0.8039218135680.0982129290043-0.1663356521851.569340380260.01179795829-0.281889385278-0.2381614198460.209995337442-0.1212791079560.06392595969220.1920920572070.06627182170320.1434443150020.4849913735160.01177807198360.02196044683920.4392807493130.007659399892140.79193050508111.771-15.278-31.591
80.08259074115350.310725500334-0.2989554595173.664577277560.10515560752.99363258502-0.1828661315710.3521098953140.125029984189-0.2945022350080.01907504173720.1000743629760.3816226051730.2745505083760.130061884430.4368126743960.103468365415-0.03023496908020.609525806398-0.01060277146890.6874680019337.847-2.65-47.691
92.530569733250.7772123590420.1923611745512.70685184045-0.273467238281.31444696566-0.2214467827720.1290162776350.09013290875820.08434834221070.1932312111760.489824033372-0.0304460818399-0.1570488697690.05986969012120.3285558754260.002635036229210.02356954977090.269183204422-0.04721752609580.34074541612784.786-34.34915.765
100.7138369737430.08863611999460.274835507554.67629211332.533007732791.49529654032-0.184787585691-0.220209952399-0.05327102701451.754632191350.127988287534-0.268756334162-0.263937258712-0.03169934996660.09814279236121.024932900020.0869584914645-0.1851617308960.37480151029-0.08786564437270.613141896352110.413-20.06630.206
111.317999398971.167732268870.04236230421782.755861597-0.01904373385240.4366356931530.13493066874-0.05783034094970.241216157780.207404980342-0.1654103179330.0934032094161-0.1238853932480.00105678010470.04782788156940.285779847948-0.01397271075420.003531815404080.3073860729470.05966701404380.34039634710171.843-50.101-26.585
125.849933464160.06698887803972.230118595142.635988996440.558395239141.96833081218-0.1408177252750.2707194413070.0900755429338-0.289489431285-0.03730759899630.0232302711376-0.0511341278953-0.06755343038070.1603862326810.30038849843-0.01635017233930.02196601614310.3113937906060.01649194307980.12013074365661.818-77.484-41.381
137.281002919462.585038234714.195574112110.9273971236241.500765874982.43070905728-0.4039510796382.14883144006-1.38554608828-1.158373575310.535070565837-0.427645964155-0.3114594486930.73468640773-0.1230017676571.052256116170.2616157052130.3687740330130.887741947299-0.04051226087240.6425919430845.786-29.275-22.113
147.972892293883.89086990981-3.139792027469.41222417384-4.068722948582.36553641557-0.5456433722191.571041481730.0563148006181-0.6170620114960.5021540348481.73058680461.0732176089-0.3880400082530.03354552790560.567473158355-0.0460119566788-0.263656862480.569235560734-0.0245290980130.65412367600270.739-31.6974.963
153.92371511834-3.207407134433.532361652525.88644939032-2.756393552953.36217013034-0.291091288285-0.1902648312660.715876515930.6824336827590.1029256054780.246097234188-0.285471216205-0.2171544241210.01459853873240.393740312391-0.06753582016410.1405492549250.543644880277-0.05783713260380.47214180795666.211-36.254-14.416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:106 )B1 - 106
2X-RAY DIFFRACTION2( CHAIN B AND RESID 107:212 )B107 - 212
3X-RAY DIFFRACTION3( CHAIN D AND RESID 1:106 )D1 - 106
4X-RAY DIFFRACTION4( CHAIN D AND RESID 107:211 )D107 - 211
5X-RAY DIFFRACTION5( CHAIN F AND RESID 1:106 )F1 - 106
6X-RAY DIFFRACTION6( CHAIN F AND RESID 107:212 )F107 - 212
7X-RAY DIFFRACTION7( CHAIN A AND RESID 1:122 )A1 - 122
8X-RAY DIFFRACTION8( CHAIN A AND RESID 123:213 )A123 - 213
9X-RAY DIFFRACTION9( CHAIN C AND RESID 1:122 )C1 - 122
10X-RAY DIFFRACTION10( CHAIN C AND RESID 123:213 )C123 - 213
11X-RAY DIFFRACTION11( CHAIN E AND RESID 1:122 )E1 - 122
12X-RAY DIFFRACTION12( CHAIN E AND RESID 123:214 )E123 - 214
13X-RAY DIFFRACTION13( CHAIN P AND RESID 8:12 )P8 - 12
14X-RAY DIFFRACTION14( CHAIN Q AND RESID 7:12 )Q7 - 12
15X-RAY DIFFRACTION15( CHAIN R AND RESID 5:13 )R5 - 13

+
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