[English] 日本語
Yorodumi
- PDB-7wvl: Structure of P4A2 Fab in complex with Spike-RBD from SARS-CoV-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wvl
TitleStructure of P4A2 Fab in complex with Spike-RBD from SARS-CoV-2
Components
  • P4A2 Fab Light Chain
  • P4A2 Fab heavy chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Fab / Spike-RBD / complex / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNarayanan, N. / Nair, D.T.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)Intramural grant from RCB India
CitationJournal: Plos Pathog. / Year: 2022
Title: A broadly neutralizing monoclonal antibody overcomes the mutational landscape of emerging SARS-CoV-2 variants of concern.
Authors: Parray, H.A. / Narayanan, N. / Garg, S. / Rizvi, Z.A. / Shrivastava, T. / Kushwaha, S. / Singh, J. / Murugavelu, P. / Anantharaj, A. / Mehdi, F. / Raj, N. / Singh, S. / Dandotiya, J. / ...Authors: Parray, H.A. / Narayanan, N. / Garg, S. / Rizvi, Z.A. / Shrivastava, T. / Kushwaha, S. / Singh, J. / Murugavelu, P. / Anantharaj, A. / Mehdi, F. / Raj, N. / Singh, S. / Dandotiya, J. / Lukose, A. / Jamwal, D. / Kumar, S. / Chiranjivi, A. / Dhyani, S. / Mishra, N. / Kumar, S. / Jakhar, K. / Sonar, S. / Panchal, A.K. / Tripathy, M.R. / Chowdhury, S.R. / Ahmed, S. / Samal, S. / Mani, S. / Bhattacharyya, S. / Das, S. / Sinha, S. / Luthra, K. / Batra, G. / Sehgal, D. / Medigeshi, G.R. / Sharma, C. / Awasthi, A. / Garg, P.K. / Nair, D.T. / Kumar, R.
History
DepositionFeb 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: P4A2 Fab Light Chain
H: P4A2 Fab heavy chain
F: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)71,5353
Polymers71,5353
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-29 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.309, 85.309, 205.193
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Antibody P4A2 Fab Light Chain


Mass: 23897.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody P4A2 Fab heavy chain


Mass: 22536.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein Spike protein S1 / S GLYCOPROTEIN / E2 / PEPLOMER PROTEIN / SPIKE GLYCOPROTEIN


Mass: 25101.059 Da / Num. of mol.: 1 / Fragment: Receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.01 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20% Peg 5K MME, 0.2 M Magnesium formate

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 3→73.88 Å / Num. obs: 18080 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 91.67 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.3
Reflection shellResolution: 3→3.24 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3650 / CC1/2: 0.79 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLM7.3.0data reduction
Aimless7.1.012data scaling
PHASER7.1.012phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7b3o

7b3o


Resolution: 3→73.88 Å / SU ML: 0.6117 / Cross valid method: FREE R-VALUE / σ(F): 0.7 / Phase error: 30.116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2794 1375 7.56 %
Rwork0.2326 30770 -
obs0.236 17972 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.53 Å2
Refinement stepCycle: LAST / Resolution: 3→73.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4567 0 0 60 4627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324677
X-RAY DIFFRACTIONf_angle_d0.67736377
X-RAY DIFFRACTIONf_chiral_restr0.0416712
X-RAY DIFFRACTIONf_plane_restr0.0046829
X-RAY DIFFRACTIONf_dihedral_angle_d14.15141642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.060.52691580.47741716X-RAY DIFFRACTION98.84
3.06-3.120.55851390.42651670X-RAY DIFFRACTION99.07
3.12-3.190.39781440.33481702X-RAY DIFFRACTION99.03
3.19-3.260.37541430.32941708X-RAY DIFFRACTION98.88
3.26-3.340.33711260.28661702X-RAY DIFFRACTION99.56
3.34-3.430.37611640.29831701X-RAY DIFFRACTION99.1
3.43-3.540.35091610.29961673X-RAY DIFFRACTION99.3
3.54-3.650.36371300.32131712X-RAY DIFFRACTION99.51
3.65-3.780.39161700.26571679X-RAY DIFFRACTION99.36
3.78-3.930.3635950.24241748X-RAY DIFFRACTION99.3
3.93-4.110.2821240.21241754X-RAY DIFFRACTION99.47
4.11-4.330.22151540.2051688X-RAY DIFFRACTION99.51
4.33-4.60.19631450.19561681X-RAY DIFFRACTION99.56
4.6-4.950.22091350.17361731X-RAY DIFFRACTION99.84
4.96-5.450.22241640.18821701X-RAY DIFFRACTION100
5.45-6.230.21461340.2251696X-RAY DIFFRACTION99.89
6.24-7.860.23071190.21731765X-RAY DIFFRACTION100
7.87-73.880.27011100.19621743X-RAY DIFFRACTION99.95
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)
10.2648035265790.2304895492480.1415833815682.12496279184-2.451111807672.63258563305-0.1553763494981.2448347965-1.09411144069-0.356225893643-0.372638871517-0.4171835448270.5547929291940.657392064890.7290120966810.6845467380660.08850932107340.2757962434121.29810465722-0.5529141094521.603708040353.5409889473-28.1384523025100.470154811
21.78186935698-1.17346149202-0.9601238114483.60631734894-0.6406229795476.4669393994-0.00254292412753-0.523126233382-0.365939571867-0.062700753313-0.126650098473-0.634058951031-0.06831137175571.02768620181-0.05351477899970.392855267971-0.0673329793625-0.04587488626450.726228448702-0.09167674826850.63085345212873.1380695236-2.8892950996397.221685118
31.06360885735-1.66036068527-1.981916459794.12655510001-1.1963291414.897738642450.01387662199330.00457888799337-0.1496754999750.18774381513-0.0153189578142-0.1094033974170.2352172314420.4972730615770.05842079397730.555292726602-0.0854567256371-0.02170071941430.699637164979-0.07891503180890.60580183486564.7901928794-5.87187028184104.494122155
42.048481310290.443703792512-0.06688327915775.459671487693.202213284072.266971124850.112269165080.0171812314779-0.14035186429-0.258704962807-0.07143093348380.0508744324933-0.0625347441101-0.147800491319-0.04592808830890.392863919624-0.03186520502980.01403031867410.751152637549-0.1237059293020.71587614068364.3079023409-3.203207155894.474664909
51.175736937790.5072382578210.1701595510870.950930983908-1.266391618082.745762528190.07299563745430.0338170415698-0.05351194940430.04255993889580.0271624479832-0.00194949362249-0.3269314686210.240777339401-0.1466343456380.612624803567-0.04611971755480.05082127244660.650355702043-0.1903702762830.49045757189863.138139461811.615767232582.5821512758
61.69760374221-1.70675966018-0.2848671564913.80284698911-1.862709958044.141055613190.13692456231-0.1209556976210.3771884197080.0334411971649-0.249260758370.0634290371217-0.4979445095980.519951377426-0.1504329523910.703571237427-0.1622565293030.07950580091350.74065657798-0.244893814560.66534394391666.600596782216.461979128774.9792861718
72.10840310627-1.01816715176-0.2574579987782.95663113852-0.03012429019291.840571430690.5941861327540.3005050012660.411001221721-0.729060893755-0.275906733084-0.291555123139-0.628623867730.0373812039556-0.2304892165020.857795779789-0.04688760016070.1169552777740.800732562889-0.0591564689990.71905354656564.166512235923.19578463566.6383075574
81.555032464720.1327549987720.01125002106346.12329436652-3.521688483624.603673294530.37866443908-0.3211813544890.3275345115781.12475025645-0.09602236563830.281736752445-0.6569964454450.0040326405701-0.274986674180.671491406968-0.1168536762620.1788418741170.611714150033-0.1989791407120.62256017293954.227451507613.5832821736108.452332408
93.39961693911-1.63231995342-1.232421910194.535486166870.5204261370145.041137695710.2716925406060.458261836324-0.30368228761-0.356178510978-0.3717951584940.708331975328-0.145548045909-0.3988687824890.08412952098990.581091881892-0.01643162715510.04662678391480.729823730353-0.1407307949230.72509749287949.889289419917.952274741278.2462104707
10-0.0792730699036-0.394488724582-0.1488476909716.278684100583.565700157466.086735756060.721732175394-0.0449777305994-0.724711266279-1.09246001425-0.9131849701341.35004947791-0.283728982725-0.3645595697310.1855979752380.873062326148-0.03920922405970.2435911585521.10018357933-0.4613474239931.7276876309342.185379383-36.1869698371108.738807655
110.290847037979-0.0763117557753-0.3093565047570.01619863930050.06059563017841.04285084323-0.3203425075930.321982517494-1.552656856431.625971826671.1138523611-0.8392830705750.557581200334-0.306088709027-0.2254289989421.911722486-0.2930475176750.6693609321360.822274246103-0.2083857578162.2000874391747.1312137159-40.5412695638116.331262665
121.87832572639-0.783153807299-0.5248189631337.77901504159-5.008262336533.37152995172-0.6446409325470.712421165227-1.483246897320.2670940106010.343435909331-2.722567934111.987158634450.5689694993240.3975090333931.907269049450.2982642370740.1591062433231.30422317269-0.4866902965392.0473546983755.6835297719-47.0842243601107.137629105
131.72038669807-0.4428933990170.9460492577072.518650751382.480755842713.402876462140.638676155587-0.041136988228-0.9458832227291.029009282490.676966455238-0.6363759882931.905356557651.10565843984-0.0269632175821.037585681080.1188781174790.05368463309220.700161275405-0.1129008893181.9377347644351.7702937593-38.0127698831114.844088835
144.059335955660.4319863755671.266508419666.664562072673.200520853383.4454568359-0.9226441561741.51154779651-2.61066480596-0.0762278380160.795970724002-1.34672289470.3981406114081.19079642479-0.4269345955610.7416903815570.06636515268870.3765097354281.15562567557-0.4404211132911.7898457415762.0383022262-27.5886266032110.14231494
152.517516186820.775431964595-0.1785808516942.171188487421.28721164823.49167261834-0.1546722567870.115126966033-1.364372100350.07446252256610.11012063957-0.1969274009770.7426993965790.446324612025-0.2264305948170.8369836582650.07436831565240.217024111690.734719169966-0.0742923913051.1040114899353.6060526514-27.1705881627111.788725103
161.450581245631.061630951370.324145781012.66849949764-0.1908242785920.151008935188-0.422272980821-0.549776624637-0.1474375597530.8665304196760.367050674111-0.5453731063310.1181401330870.03762303324180.1297719751821.14184519552-0.06781789765130.03961904946380.762939038325-0.1111962226960.65497163402556.6944440618-5.91179980658119.554045729
170.4491698595570.6708748970091.063291176080.9494271788412.001210603743.16830484286-0.269176461961.00404294755-1.0414465589-0.245905069403-0.1353679617470.571086550836-0.249153951372-0.2359409646420.560663274330.739685902411-0.1367682999580.3055516902421.25752623241-0.4456736032981.0742105991750.639293464-17.7402745349105.541572419
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'F' and (resid 500 through 513 )FC500 - 513164 - 177
22chain 'L' and (resid 1 through 25 )LA1 - 251 - 25
33chain 'L' and (resid 26 through 79 )LA26 - 7926 - 79
44chain 'L' and (resid 80 through 94 )LA80 - 9480 - 94
55chain 'L' and (resid 95 through 148 )LA95 - 14895 - 148
66chain 'L' and (resid 149 through 178 )LA149 - 178149 - 178
77chain 'L' and (resid 179 through 216 )LA179 - 216179 - 216
88chain 'H' and (resid 1 through 119 )HB1 - 1191 - 119
99chain 'H' and (resid 120 through 212 )HB120 - 212120 - 212
1010chain 'F' and (resid 337 through 349 )FC337 - 3491 - 13
1111chain 'F' and (resid 350 through 367 )FC350 - 36714 - 31
1212chain 'F' and (resid 368 through 389 )FC368 - 38932 - 53
1313chain 'F' and (resid 390 through 403 )FC390 - 40354 - 67
1414chain 'F' and (resid 404 through 421 )FC404 - 42168 - 85
1515chain 'F' and (resid 422 through 469 )FC422 - 46986 - 133
1616chain 'F' and (resid 470 through 489 )FC470 - 489134 - 153
1717chain 'F' and (resid 490 through 499 )FC490 - 499154 - 163

+
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