[English] 日本語
Yorodumi
- PDB-7n3d: Crystal Structure of Human Fab S24-1564 in the complex with the N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n3d
TitleCrystal Structure of Human Fab S24-1564 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2
Components
  • (S24-1564 Fab ...) x 2
  • Nucleoprotein
KeywordsVIRAL PROTEIN / SARS Coronavirus 2 / Nucleocapsid protein / Human antibody Fab / COVID-19 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways ...response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / VEGFR2 mediated vascular permeability / molecular condensate scaffold activity / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / DDX58/IFIH1-mediated induction of interferon-alpha/beta / MHC class I protein complex / RNA stem-loop binding / Interleukin-1 signaling / Interferon alpha/beta signaling / viral capsid / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / Induction of Cell-Cell Fusion / Attachment and Entry / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / RNA binding / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Immunoglobulins ...Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsKim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Dugan, H. / Stamper, C. / Wilson, P. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Iscience / Year: 2024
Title: Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies.
Authors: Kim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Endres, M. / Ma, H. / Dugan, H.L. / Stamper, C.T. / Chang, C. / Li, L. / Changrob, S. / Zheng, N.Y. / Huang, M. / Ramanathan, A. / ...Authors: Kim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Endres, M. / Ma, H. / Dugan, H.L. / Stamper, C.T. / Chang, C. / Li, L. / Changrob, S. / Zheng, N.Y. / Huang, M. / Ramanathan, A. / Wilson, P. / Michalska, K. / Joachimiak, A.
History
DepositionMay 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Feb 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 1.4Oct 23, 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
H: S24-1564 Fab heavy chain
L: S24-1564 Fab light chain
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,31616
Polymers61,6693
Non-polymers64713
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-56 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.927, 67.318, 86.087
Angle α, β, γ (deg.)90.000, 106.643, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 1 molecules C

#3: Protein Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 14303.961 Da / Num. of mol.: 1 / Fragment: CoV N NTD domain, residues 47-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: P0DTC9

-
Antibody , 2 types, 2 molecules HL

#1: Antibody S24-1564 Fab heavy chain


Mass: 23950.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody S24-1564 Fab light chain


Mass: 23413.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

-
Non-polymers , 3 types, 407 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 81619 / % possible obs: 95.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 21.23 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.114 / Net I/σ(I): 22
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 2795 / CC1/2: 0.412 / % possible all: 66.2

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBIDs 5KKU, 5O4G, 6IEB

5kku

5o4g

6ieb


Resolution: 1.53→39.51 Å / SU ML: 0.1753 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.7602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1902 3930 4.82 %
Rwork0.1572 77630 -
obs0.1588 81560 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.84 Å2
Refinement stepCycle: LAST / Resolution: 1.53→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 34 394 4592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00944640
X-RAY DIFFRACTIONf_angle_d1.0156351
X-RAY DIFFRACTIONf_chiral_restr0.0634695
X-RAY DIFFRACTIONf_plane_restr0.0078838
X-RAY DIFFRACTIONf_dihedral_angle_d13.4671695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.3202800.26721471X-RAY DIFFRACTION50.77
1.54-1.560.27411150.27092033X-RAY DIFFRACTION70.89
1.56-1.580.3044920.26322451X-RAY DIFFRACTION83.54
1.58-1.60.30871420.24642646X-RAY DIFFRACTION90.76
1.6-1.620.30281110.23462763X-RAY DIFFRACTION94.6
1.62-1.650.32351330.24162810X-RAY DIFFRACTION96.43
1.65-1.670.31331560.20772806X-RAY DIFFRACTION98.27
1.67-1.70.25711470.19042885X-RAY DIFFRACTION98.67
1.7-1.730.22761560.17792851X-RAY DIFFRACTION98.82
1.73-1.760.21351170.15952912X-RAY DIFFRACTION99.12
1.76-1.80.22221440.15472891X-RAY DIFFRACTION98.86
1.8-1.830.20731470.1482838X-RAY DIFFRACTION98.51
1.83-1.870.18551490.14112885X-RAY DIFFRACTION99.48
1.87-1.920.19161480.13692901X-RAY DIFFRACTION99.64
1.92-1.960.20071320.14212920X-RAY DIFFRACTION99.32
1.96-2.020.17741520.13682847X-RAY DIFFRACTION99.37
2.02-2.080.16981380.14792871X-RAY DIFFRACTION99.01
2.08-2.140.18941640.14042881X-RAY DIFFRACTION98.67
2.14-2.220.1891450.13812881X-RAY DIFFRACTION98.09
2.22-2.310.17471680.14252850X-RAY DIFFRACTION99.57
2.31-2.410.18981310.14412931X-RAY DIFFRACTION99.64
2.41-2.540.19611680.15642890X-RAY DIFFRACTION99.51
2.54-2.70.20511410.15732858X-RAY DIFFRACTION98.55
2.7-2.910.18581400.16842870X-RAY DIFFRACTION97.89
2.91-3.20.18211680.16182915X-RAY DIFFRACTION99.48
3.2-3.660.19921490.15362905X-RAY DIFFRACTION99.61
3.66-4.610.13791530.142893X-RAY DIFFRACTION98.26
4.61-39.510.18291440.15962975X-RAY DIFFRACTION98.67

+
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