[English] 日本語
Yorodumi
- PDB-7rlz: Antibody 2F2 in complex with P. vivax CSP peptide GDRAAGQPAGNGAGGQAA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rlz
TitleAntibody 2F2 in complex with P. vivax CSP peptide GDRAAGQPAGNGAGGQAA
Components
  • 2F2 Fab heavy chain
  • 2F2 Fab light chain
  • peptide from Circumsporozoite protein variant VK210
KeywordsANTIMICROBIAL PROTEIN / antibody / malaria / Plasmodium vivax / circumsporozoite protein
Function / homology
Function and homology information


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
Circumsporozoite protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Plasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 Å
AuthorsKucharska, I. / Julien, J.P.
Funding support Canada, 4items
OrganizationGrant numberCountry
Other governmentOntario Early Researcher Awards program Canada
Other governmentCanada Foundation for Innovation Canada
Other governmentOntario Research Fund Canada
Other governmentCanada Research Chairs Canada
CitationJournal: Elife / Year: 2022
Title: Structural basis of Plasmodium vivax inhibition by antibodies binding to the circumsporozoite protein repeats.
Authors: Kucharska, I. / Hossain, L. / Ivanochko, D. / Yang, Q. / Rubinstein, J.L. / Pomes, R. / Julien, J.P.
History
DepositionJul 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: peptide from Circumsporozoite protein variant VK210
B: 2F2 Fab light chain
A: 2F2 Fab heavy chain
C: 2F2 Fab light chain
D: 2F2 Fab heavy chain
R: peptide from Circumsporozoite protein variant VK210


Theoretical massNumber of molelcules
Total (without water)99,7156
Polymers99,7156
Non-polymers00
Water1,802100
1
P: peptide from Circumsporozoite protein variant VK210
B: 2F2 Fab light chain
A: 2F2 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)49,8583
Polymers49,8583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 2F2 Fab light chain
D: 2F2 Fab heavy chain
R: peptide from Circumsporozoite protein variant VK210


Theoretical massNumber of molelcules
Total (without water)49,8583
Polymers49,8583
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.360, 60.490, 159.060
Angle α, β, γ (deg.)90.000, 101.219, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 3 through 214)
d_2ens_1chain "D"
d_1ens_2(chain "B" and (resid 1 through 9 or resid 11 through 26 or resid 27A through 213))
d_2ens_2(chain "C" and (resid 1 through 9 or resid 11 through 26 or resid 27A through 213))
d_1ens_3chain "P"
d_2ens_3chain "R"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNLYSC1 - 220
d_21ens_1GLNLYSE1 - 220
d_11ens_2ASPLEUB1 - 9
d_12ens_2LEUSERB11 - 26
d_13ens_2SERGLUB28 - 218
d_21ens_2ASPLEUD1 - 9
d_22ens_2LEUSERD11 - 26
d_23ens_2SERGLUD28 - 218
d_11ens_3ASPASNA1 - 10
d_21ens_3ASPASNF1 - 10

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.996768280681, -0.0376489744572, 0.0709616047611), (-0.0423089824435, 0.996964868058, -0.0653529024749), (-0.0682857571719, -0.0681440135275, -0.995335847233)30.6231152507, -25.9351463732, 79.2257584016
2given(-0.998145285493, -0.00389124653283, 0.0607523435656), (-0.00826885976432, 0.99737233591, -0.0719725608838), (-0.060312643836, -0.0723414249403, -0.995554671141)30.8488407469, -26.919788444, 79.1071247661
3given(-0.992971514117, -0.0540163854721, 0.105308130039), (-0.0659059011358, 0.991417524765, -0.112905729635), (-0.0983055662071, -0.119052600515, -0.988009359249)29.1581638169, -24.1043740335, 79.5846125859

-
Components

#1: Protein/peptide peptide from Circumsporozoite protein variant VK210 / CS


Mass: 1526.550 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Plasmodium vivax (malaria parasite P. vivax)
References: UniProt: P08677
#2: Antibody 2F2 Fab light chain


Mass: 24284.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody 2F2 Fab heavy chain


Mass: 24046.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M di-sodium tartrate and 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033167 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.25→29.69 Å / Num. obs: 41601 / % possible obs: 99.9 % / Redundancy: 11.6 % / Biso Wilson estimate: 50.02 Å2 / CC1/2: 0.927 / Net I/σ(I): 9.4
Reflection shellResolution: 2.25→2.32 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3874 / CC1/2: 0.435

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.27→29.69 Å / SU ML: 0.3138 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8397
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2387 2026 5 %
Rwork0.1914 38476 -
obs0.1938 40502 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.74 Å2
Refinement stepCycle: LAST / Resolution: 2.27→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6832 0 0 100 6932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327009
X-RAY DIFFRACTIONf_angle_d0.70739532
X-RAY DIFFRACTIONf_chiral_restr0.04641067
X-RAY DIFFRACTIONf_plane_restr0.00451214
X-RAY DIFFRACTIONf_dihedral_angle_d11.13272510
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.876363208918
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.631436664896
ens_3d_2AX-RAY DIFFRACTIONTorsion NCS1.03148168901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.330.3451460.2822759X-RAY DIFFRACTION100
2.33-2.390.37641420.27972702X-RAY DIFFRACTION100
2.39-2.460.35211420.26812709X-RAY DIFFRACTION100
2.46-2.540.30641460.25712768X-RAY DIFFRACTION100
2.54-2.630.29731440.24092730X-RAY DIFFRACTION100
2.63-2.740.28751430.22852712X-RAY DIFFRACTION100
2.74-2.860.28651430.22812728X-RAY DIFFRACTION100
2.86-3.010.26661450.2372744X-RAY DIFFRACTION100
3.01-3.20.2571450.21462748X-RAY DIFFRACTION100
3.2-3.450.28981440.19782759X-RAY DIFFRACTION100
3.45-3.790.25021450.18952743X-RAY DIFFRACTION100
3.79-4.340.18891440.16282780X-RAY DIFFRACTION99.86
4.34-5.460.17951470.14382762X-RAY DIFFRACTION99.56
5.46-29.690.20611500.16962832X-RAY DIFFRACTION99.2
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)
10.803418717364-0.539446097923-1.33005402890.891907003041.161694411612.91092988273-0.37254896135-0.0356225750505-0.2551409248960.6114106289950.154812001452-1.2878065243-0.3219215894630.1116867124350.3655321922680.6422443909090.0322441656246-0.09777276492510.5184281793820.0697577163980.70755081078520.3499146895-41.004405797684.3314529916
20.1457340215330.115870356282-0.2489813677371.442069883820.3120603292890.524697333018-0.341448886358-0.199626522967-1.08186408151-0.1298866252850.139261897035-0.6515742595120.684631535959-0.132336141424-0.00896212017240.6597105565530.005321054575390.08453107240120.6878443843680.006884250862730.68181640978519.0571134468-31.746137584337.0481732034
32.2797007814-1.8211174571-0.6206173392616.197628230060.4448545696510.1540283253560.765775456083-0.1953122242080.22920645614-0.9307334709050.470596652757-1.048474812441.340187569660.1409298944220.2765605602640.954933708883-0.0911760136247-0.1430762703560.5092189657420.1923203557160.085919899389214.72734134-1.9737214829141.8499644221
44.046183898040.000585683212033-0.1222145927361.440399933860.6010363352143.289716843230.0499460640561-0.3014898517180.06186533553240.236157177654-0.0715522098049-0.0667462252128-0.004706609456690.141929748495-0.04201211859160.594699673072-0.0216978183519-0.03991811942590.4269839939980.03708528578240.34496216630831.5031601865-0.31344546192429.4782541767
52.72521310483-0.6370314297242.091543306151.37828871112-0.478200180956.636835353680.1666753522980.4459291868090.0566377706096-0.304869493146-0.14929446806-0.1010611886050.150184433840.513714245554-0.0170924064270.5201078517580.02852326101-0.03119845217770.329572656614-0.01770190330120.35910334945928.676225816-3.24042735758-8.31306375385
63.327523651240.3630674033880.7269188636292.88342848985-0.2413481152244.146865493720.221633411882-0.478136247778-0.321904377050.0076662121451-0.05171505626660.4917945185740.563178671926-0.475640181350.02699727005220.453334632135-0.00842467157774-0.0007824054560140.3898704399210.02895195398710.3544118351497.93317176817-3.4844501256924.796852251
74.473154102290.1862710057070.2595953280091.88654794619-1.472881884174.243071151860.0810497945243-0.4824795975620.2514849205120.251717161584-0.04019080724060.250794380966-0.0702520610428-0.2929289300670.0586539048840.550112544374-0.02609936636580.04119641357660.440956248942-0.08308494106070.35852555541611.33171728980.7017126704428.3623538721
83.430914551-1.99117346765-1.120456257954.764720734510.9832570513541.375334479710.05466816581890.08205893330650.0740879659347-0.100703893208-0.0245970755842-0.0497493875253-0.030703999061-0.0003491991257130.0252896274850.462830579111-0.0134847576507-0.1057937534160.324963967737-0.01166517414830.31522351717416.7827721915-9.56868302958-1.74807485399
91.96461912497-1.11863375243-0.5759480578943.73238948462-0.7915037741783.113606971130.65112973161.09228759672-0.14357596134-0.758709922272-0.3558317344790.1744119340090.104463997015-1.111897296660.4455610016120.522680599536-0.00149813374069-0.1175718925830.477835802458-0.05314270889090.59333421158711.212378621-14.9753475963-6.2592582575
102.825129548270.299270178614-2.37801561210.328695597281-1.471159617418.61706763316-0.1216593561160.373778975857-0.192832583235-0.2772192132110.0645209047391-0.08431809890940.261710163927-0.109100513579-0.001450005143180.487254833838-0.0331264223838-0.08445155319480.380165745950.02082890069740.384907667877-0.301040194804-30.923720041348.1616753567
111.24640862010.1394622589990.2466574664690.6359043076690.5651135135872.776730386560.0878158856651-0.1422628567040.02444723819130.115306889966-0.0893192995186-0.102565264309-0.05564419925610.223112027935-0.0248922723870.379321904124-0.00961175094075-0.06385456306260.2748322062440.01499495053740.3026043790245.22229437089-29.589262306767.3654343232
122.446507668890.7870683116550.8714920540772.278526340731.285030130264.436876382550.0879651209435-0.2837095613090.1174910540920.309379315769-0.0875304195850.01387677445830.106701387506-0.000367726140703-0.0428231671350.474915104776-0.00400887680015-0.03363449412470.3198158424380.007717749368790.4236992684911.26358435447-28.610607025787.32105848
132.36300162570.2539775025240.5198073432254.878209309561.436091724745.979828420240.04713168038950.48811025581-0.254744488861-0.322164813149-0.101738773274-0.3014238665740.2451624793440.3736404236140.07808008656020.327101651306-0.01445224371870.02848727024290.4412307239540.03823903719260.39797070327823.0233255387-29.367731376751.960126171
143.18028036142.110022737410.4875069874311.905942014141.109828247077.40645709826-0.2451672057160.743870306790.983380369533-0.3759372674450.751903359452-0.585253816717-1.338871425450.6893004739780.09054489623080.59510420421-0.0425426869787-0.005238554330760.6016287428950.2119462361420.58218040612125.9256221885-21.253463488648.4295115844
152.519629609870.820220664947-1.059195387131.456084390272.347506624588.412708548550.02892949673920.01024004486580.562498843711-0.1189154091860.305178452539-0.22328446651-0.4897011601470.680779411336-0.1197846267620.50455415637-0.040727644063-0.0003399605400710.6747394101150.07659574150720.6544058788527.687228208-24.835264430455.2238462573
160.8296007322420.2187608829110.4110895988760.844278458174-0.04094119098622.8980279046-0.1085079055840.0324102442503-0.074403440579-0.0786717079897-0.0423672089363-0.241341010673-0.1022495469340.2679223920840.242420257860.3782097965010.027250007632-0.03655259205170.267908393838-0.01001541620920.41549366079714.9289122248-33.784273367967.2680019053
172.758717480031.073204168620.4273249063163.09685971193-1.215072792382.05894230252-0.054486692977-0.0987749139782-0.05280084117240.1279831214930.020547224289-0.06366249448930.09125265314360.1579294630020.09298774124830.429426129345-0.00358749424859-0.05551767770610.292621282597-0.04468871039950.41431495912614.3316930975-36.954592838378.1318282887
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 204 through 214 )DE204 - 214210 - 220
22chain 'R' and (resid 2 through 11 )RF2 - 111 - 10
33chain 'P' and (resid 2 through 11 )PA2 - 111 - 10
44chain 'B' and (resid 1 through 101 )BB1 - 1011 - 106
55chain 'B' and (resid 102 through 213 )BB102 - 213107 - 218
66chain 'A' and (resid 3 through 39 )AC3 - 391 - 37
77chain 'A' and (resid 40 through 111 )AC40 - 11138 - 117
88chain 'A' and (resid 112 through 203 )AC112 - 203118 - 209
99chain 'A' and (resid 204 through 215 )AC204 - 215210 - 221
1010chain 'C' and (resid 1 through 83 )CD1 - 831 - 88
1111chain 'C' and (resid 84 through 128 )CD84 - 12889 - 133
1212chain 'C' and (resid 129 through 213 )CD129 - 213134 - 218
1313chain 'D' and (resid 3 through 59 )DE3 - 591 - 58
1414chain 'D' and (resid 60 through 72 )DE60 - 7259 - 71
1515chain 'D' and (resid 73 through 87 )DE73 - 8772 - 89
1616chain 'D' and (resid 88 through 145 )DE88 - 14590 - 151
1717chain 'D' and (resid 146 through 203 )DE146 - 203152 - 209

+
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