[English] 日本語
Yorodumi
- PDB-8f5i: SARS-CoV-2 S2 helix epitope scaffold bound by antibody DH1057.1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f5i
TitleSARS-CoV-2 S2 helix epitope scaffold bound by antibody DH1057.1
Components
  • DH1057.1 HC
  • DH1057.1 LC
  • Specialized acyl carrier protein
KeywordsIMMUNE SYSTEM / epitope scaffold / S2 helix / DH1057.1 / Fab / spike
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / membrane / cytosol
Similarity search - Function
Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Acyl carrier protein AcpXL
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKapingidza, A.B. / Wrapp, D. / Winters, K. / Azoitei, M.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1P01AI158571-01A1 United States
CitationJournal: Nat Commun / Year: 2023
Title: Engineered immunogens to elicit antibodies against conserved coronavirus epitopes.
Authors: Kapingidza, A.B. / Marston, D.J. / Harris, C. / Wrapp, D. / Winters, K. / Mielke, D. / Xiaozhi, L. / Yin, Q. / Foulger, A. / Parks, R. / Barr, M. / Newman, A. / Schafer, A. / Eaton, A. / ...Authors: Kapingidza, A.B. / Marston, D.J. / Harris, C. / Wrapp, D. / Winters, K. / Mielke, D. / Xiaozhi, L. / Yin, Q. / Foulger, A. / Parks, R. / Barr, M. / Newman, A. / Schafer, A. / Eaton, A. / Flores, J.M. / Harner, A. / Catanzaro Jr., N.J. / Mallory, M.L. / Mattocks, M.D. / Beverly, C. / Rhodes, B. / Mansouri, K. / Van Itallie, E. / Vure, P. / Dunn, B. / Keyes, T. / Stanfield-Oakley, S. / Woods, C.W. / Petzold, E.A. / Walter, E.B. / Wiehe, K. / Edwards, R.J. / Montefiori, D.C. / Ferrari, G. / Baric, R. / Cain, D.W. / Saunders, K.O. / Haynes, B.F. / Azoitei, M.L.
History
DepositionNov 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Specialized acyl carrier protein
B: Specialized acyl carrier protein
H: DH1057.1 HC
L: DH1057.1 LC
X: DH1057.1 HC
Y: DH1057.1 LC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8098
Polymers118,1506
Non-polymers1,6602
Water24,3741353
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.680, 76.360, 79.020
Angle α, β, γ (deg.)71.60, 69.99, 88.30
Int Tables number1
Space group name H-MP1

-
Components

-
Antibody , 2 types, 4 molecules HXLY

#2: Antibody DH1057.1 HC


Mass: 24102.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody DH1057.1 LC


Mass: 23638.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Protein / Non-polymers , 2 types, 1355 molecules AB

#1: Protein Specialized acyl carrier protein


Mass: 11333.716 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA2022 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N882
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1353 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45.68 Å / Num. obs: 88193 / % possible obs: 93.87 % / Redundancy: 4.7 % / CC1/2: 0.474 / Net I/σ(I): 29.11
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.21 / Num. unique obs: 8122 / CC1/2: 0.207 / % possible all: 87.6

-
Processing

Software
NameVersionClassification
PHENIXdev-3758refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LMO

3lmo


Resolution: 1.9→45.68 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 4316 4.96 %
Rwork0.2112 --
obs0.2129 87026 93.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8003 0 111 1353 9467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088296
X-RAY DIFFRACTIONf_angle_d0.86211286
X-RAY DIFFRACTIONf_dihedral_angle_d25.6842999
X-RAY DIFFRACTIONf_chiral_restr0.0621307
X-RAY DIFFRACTIONf_plane_restr0.0051436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.4631300.43392430X-RAY DIFFRACTION84
1.92-1.940.38661440.35622612X-RAY DIFFRACTION89
1.94-1.970.35211270.34572650X-RAY DIFFRACTION90
1.97-1.990.33061480.29472639X-RAY DIFFRACTION91
1.99-2.020.3031300.26362708X-RAY DIFFRACTION91
2.02-2.050.28411280.25152666X-RAY DIFFRACTION91
2.05-2.080.28561430.2482700X-RAY DIFFRACTION92
2.08-2.110.27181340.24372754X-RAY DIFFRACTION92
2.11-2.140.28191320.23042686X-RAY DIFFRACTION93
2.14-2.170.2491510.23162836X-RAY DIFFRACTION95
2.17-2.210.33531370.27742725X-RAY DIFFRACTION94
2.21-2.250.45561360.35192788X-RAY DIFFRACTION94
2.25-2.30.38891140.30552723X-RAY DIFFRACTION92
2.3-2.340.30071750.24862785X-RAY DIFFRACTION95
2.34-2.390.28591520.2272802X-RAY DIFFRACTION95
2.39-2.450.28411500.22632784X-RAY DIFFRACTION95
2.45-2.510.2421410.22172780X-RAY DIFFRACTION95
2.51-2.580.2541630.21642799X-RAY DIFFRACTION95
2.58-2.650.26391470.21322799X-RAY DIFFRACTION95
2.65-2.740.25691640.2072803X-RAY DIFFRACTION95
2.74-2.840.25161350.20512845X-RAY DIFFRACTION96
2.84-2.950.21391660.20622757X-RAY DIFFRACTION96
2.95-3.090.25831320.19692832X-RAY DIFFRACTION96
3.09-3.250.20441430.18442819X-RAY DIFFRACTION96
3.25-3.450.19281480.17782851X-RAY DIFFRACTION96
3.45-3.720.21011340.18192808X-RAY DIFFRACTION96
3.72-4.090.18071310.16952863X-RAY DIFFRACTION96
4.09-4.680.16961730.14082820X-RAY DIFFRACTION97
4.68-5.90.18371560.15662820X-RAY DIFFRACTION97
5.9-45.680.19011520.16652826X-RAY DIFFRACTION96

+
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