[English] 日本語
Yorodumi
- PDB-7mfv: Crystal structure of synthetic nanobody (Sb16) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mfv
TitleCrystal structure of synthetic nanobody (Sb16)
ComponentsSynthetic Nanobody #16 (Sb16)
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / Spike Protein / RBD / Antibody / Nanobody / Sybody / VIRAL PROTEIN / epitope / neutralization
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJiang, J. / Ahmad, J. / Natarajan, K. / Boyd, L.F. / Margulies, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Citation
Journal: J Biol Chem / Year: 2021
Title: Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction.
Authors: Javeed Ahmad / Jiansheng Jiang / Lisa F Boyd / Allison Zeher / Rick Huang / Di Xia / Kannan Natarajan / David H Margulies /
Abstract: Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of ...Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of antibodies with the SARS-CoV-2 receptor-binding domain (RBD). Here, we report five X-ray crystal structures of sybodies (synthetic nanobodies) including those of binary and ternary complexes of Sb16-RBD, Sb45-RBD, Sb14-RBD-Sb68, and Sb45-RBD-Sb68, as well as unliganded Sb16. These structures reveal that Sb14, Sb16, and Sb45 bind the RBD at the angiotensin-converting enzyme 2 interface and that the Sb16 interaction is accompanied by a large conformational adjustment of complementarity-determining region 2. In contrast, Sb68 interacts at the periphery of the SARS-CoV-2 RBD-angiotensin-converting enzyme 2 interface. We also determined cryo-EM structures of Sb45 bound to the SARS-CoV-2 spike protein. Superposition of the X-ray structures of sybodies onto the trimeric spike protein cryo-EM map indicates that some sybodies may bind in both "up" and "down" configurations, but others may not. Differences in sybody recognition of several recently identified RBD variants are explained by these structures.
#1: Journal: Biorxiv / Year: 2021
Title: Synthetic nanobody-SARS-CoV-2 receptor-binding domain structures identify distinct epitopes.
Authors: Ahmad, J. / Jiang, J. / Boyd, L.F. / Natarajan, K. / Margulies, D.H.
History
DepositionApr 11, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionJun 2, 2021ID: 7KGL
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 2.0Sep 1, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / pdbx_audit_support / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.end_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct.title / _struct_conn.pdbx_dist_value
Description: Atomic clashes
Details: Improve: 1. Ramachandran outliers to 0% 2. Molprobity clashscore to 6.0 3. rmsd (bonds/angles) to 0.006/0.97
Provider: author / Type: Coordinate replacement
Revision 2.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Revision 2.2Oct 20, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Synthetic Nanobody #16 (Sb16)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9362
Polymers12,8741
Non-polymers621
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.920, 68.920, 107.170
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 on special symmetry positions
IDModelComponents
11B-354-

HOH

21B-358-

HOH

31B-370-

HOH

-
Components

#1: Antibody Synthetic Nanobody #16 (Sb16)


Mass: 12873.515 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21b / Production host: Escherichia coli MC1061 (bacteria)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 4000, 0.1M MES pH 6.0, 0.2M LiSO4 / PH range: 5.1 - 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 12360 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Biso Wilson estimate: 31.8 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0739 / Rpim(I) all: 0.0223 / Rrim(I) all: 0.0774 / Net I/σ(I): 15.19
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 1025 / CC1/2: 0.526 / CC star: 0.83 / % possible all: 85

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KGL

7kgl
PDB Unreleased entry


Resolution: 1.9→39.87 Å / SU ML: 0.2675 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 31.1956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2506 707 6 %
Rwork0.237 11080 -
obs0.2379 11787 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 4 70 981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006940
X-RAY DIFFRACTIONf_angle_d0.95131276
X-RAY DIFFRACTIONf_chiral_restr0.4515134
X-RAY DIFFRACTIONf_plane_restr0.0056161
X-RAY DIFFRACTIONf_dihedral_angle_d15.8849329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.050.34541260.32021978X-RAY DIFFRACTION87.27
2.05-2.250.32181350.28372112X-RAY DIFFRACTION92.39
2.25-2.580.3151410.27532209X-RAY DIFFRACTION95.68
2.58-3.250.25281450.25242288X-RAY DIFFRACTION97.55
3.25-39.870.21141600.20482493X-RAY DIFFRACTION99.25
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)
14.102365604880.5127920725670.3915681523744.125503236281.546492388142.2057506955-0.315422330714-1.27602740472-0.3104454756770.3064356788980.3124429431910.5120749367360.1584001798940.0688928789263-0.08118067991780.2566266499580.0584980317557-0.007830495370510.6468389173470.1246284545810.27234309196512.241938795419.771103410513.7532030457
25.06606883772-3.6491586659-0.4740791913634.52399141157-1.155026209117.14768871194-0.102209314976-0.997630949828-1.292991275130.5335509581810.1250271347560.7210879538750.725057404321-0.543600093797-0.01978768504590.362442319159-0.04026604138720.01781354092360.5245882514280.2752875472820.48754125030620.20371810319.2215097388613.9186770893
34.458101447492.23188555367-0.8307075999496.49707316298-4.092535583494.59096451461-0.258409671335-0.7353432359490.234631594620.494934711820.667370735595-0.416898363685-0.5122866647650.0268540592006-0.4040592634120.209621012730.0745761830826-0.01135897778680.45397418919-0.03373661216420.23716264393925.422586152124.147483164315.0468101756
45.91177185797-2.54167773741.352298027977.177419392331.200995199346.60157714251-0.187938148172-0.303379617753-0.0914537084932-0.3043748096280.123805055656-0.0384845256367-0.3360743816040.06843992918110.09196435043750.215256399673-0.04550242697750.02036503473790.2488810706260.03902236354730.1554779625223.776682778320.87221867697.41854099221
56.75726180296-4.40584738136-3.769230540218.78294072463.602918840678.18230276553-0.0951829180156-0.788772242814-0.168963981041-0.7057450109230.5898605314820.143109727854-0.2088740301960.424470078352-0.4575291717020.189772600121-0.0734019891746-0.05790270286320.2622698094710.02758419906820.22216329527916.001516263218.90446521116.43665139182
63.012967042780.2191809585981.362518650381.808942197781.102299484294.57831885384-0.169644150183-1.52307159401-1.342595084970.9182464130130.6569190326120.218995634281.09597765435-0.370419131082-0.207521544760.3664410187820.1691756585360.06738329912770.6200658495480.4214133312420.38093521285915.096775080312.554925335415.6686742326
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: B / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 33 )1 - 331 - 33
22chain 'B' and (resid 34 through 45 )34 - 4534 - 45
33chain 'B' and (resid 46 through 58 )46 - 5846 - 58
44chain 'B' and (resid 59 through 74 )59 - 7459 - 74
55chain 'B' and (resid 75 through 92 )75 - 9275 - 92
66chain 'B' and (resid 93 through 116 )93 - 11693 - 116

+
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