[English] 日本語
Yorodumi
- PDB-8sfs: High Affinity nanobodies against GFP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sfs
TitleHigh Affinity nanobodies against GFP
Components
  • Green fluorescent protein
  • LaG16
KeywordsIMMUNE SYSTEM / Nanobody / nanobodies / GFP / green fluorescent protein / high-affinity antibody variant / antibody variant / single-domain antibody
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / AMMONIUM ION / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsKetaren, N.E. / Rout, M.P. / Bonnano, J.B. / Almo, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Structure / Year: 2025
Title: Unique mechanisms to increase structural stability and enhance antigen binding in nanobodies.
Authors: Ketaren, N.E. / Fridy, P.C. / Malashkevich, V. / Sanyal, T. / Brillantes, M. / Thompson, M.K. / Oren, D.A. / Bonanno, J.B. / Sali, A. / Almo, S.C. / Chait, B.T. / Rout, M.P.
History
DepositionApr 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
A: Green fluorescent protein
B: Green fluorescent protein
D: LaG16
C: LaG16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,22439
Polymers90,2214
Non-polymers2,00335
Water3,477193
1
A: Green fluorescent protein
hetero molecules

D: LaG16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,09518
Polymers45,1112
Non-polymers98416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z+1/31
Buried area1420 Å2
ΔGint-4 kcal/mol
Surface area15850 Å2
MethodPISA
2
B: Green fluorescent protein
C: LaG16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,12921
Polymers45,1112
Non-polymers1,01819
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-5 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.772, 131.772, 153.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein / Antibody , 2 types, 4 molecules ABDC

#1: Protein Green fluorescent protein


Mass: 28784.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Antibody LaG16


Mass: 16326.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 6 types, 228 molecules

#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: H4N
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 4.27 Å3/Da / Density % sol: 71.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 1.26 M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 143927 / % possible obs: 95 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.104 / Χ2: 1.702 / Net I/σ(I): 7.6 / Num. measured all: 785910
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.37-2.424.90.91970350.903193
2.42-2.485.10.77573590.937197.5
2.48-2.545.50.82176180.926199.8
2.54-2.615.60.66275070.9791100
2.61-2.695.70.53376201.0541100
2.69-2.775.70.48475831.0841100
2.77-2.875.70.37575601.1771100
2.87-2.995.80.27875651.3121100
2.99-3.125.80.276041.6021100
3.12-3.295.80.15475791.8931100
3.29-3.495.70.12175772.2731100
3.49-3.765.70.09875872.6821100
3.76-4.145.70.08475562.9741100
4.14-4.745.70.0775683.452199.9
4.74-5.975.60.05976142.7691100
5.97-505.80.04975612.843199.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMA, 4KRN

1ema

4krn


Resolution: 2.37→45.8 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 1678 2.67 %
Rwork0.1902 --
obs0.1909 62729 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5601 0 113 193 5907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095795
X-RAY DIFFRACTIONf_angle_d0.9687821
X-RAY DIFFRACTIONf_dihedral_angle_d10.42800
X-RAY DIFFRACTIONf_chiral_restr0.057838
X-RAY DIFFRACTIONf_plane_restr0.0091006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.440.3491340.32694857X-RAY DIFFRACTION96
2.44-2.520.32711360.30454996X-RAY DIFFRACTION100
2.52-2.610.3361360.28555057X-RAY DIFFRACTION100
2.61-2.710.27891360.26285039X-RAY DIFFRACTION100
2.71-2.840.27551410.26995061X-RAY DIFFRACTION100
2.84-2.990.29841440.25685102X-RAY DIFFRACTION100
2.99-3.170.27051350.23185084X-RAY DIFFRACTION100
3.17-3.420.26171400.20745095X-RAY DIFFRACTION100
3.42-3.760.21871400.18995120X-RAY DIFFRACTION100
3.76-4.310.17041410.14975132X-RAY DIFFRACTION100
4.31-5.420.16481420.12955161X-RAY DIFFRACTION100
5.42-45.80.17381530.16135347X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 69.8743 Å / Origin y: 16.1461 Å / Origin z: -0.9756 Å
111213212223313233
T0.514 Å2-0.0966 Å20.0084 Å2-0.3851 Å2-0.0282 Å2--0.3718 Å2
L0.1277 °2-0.1749 °2-0.0997 °2-0.5198 °2-0.0436 °2--0.3583 °2
S0.0624 Å °-0.039 Å °-0.0423 Å °0.1581 Å °-0.0102 Å °0.0708 Å °-0.0309 Å °0.0389 Å °-0.0562 Å °
Refinement TLS groupSelection details: all

+
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