[English] 日本語
Yorodumi
- PDB-7e7v: Crystal structure of RSL mutant in complex with sugar Ligand -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e7v
TitleCrystal structure of RSL mutant in complex with sugar Ligand
ComponentsFucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Complex / Lectin / Fucose / Rhodamine
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / Chem-R3F / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsLi, L. / Chen, G.S.
CitationJournal: ACS Nano / Year: 2023
Title: Spatiotemporal Landscape for the Sophisticated Transformation of Protein Assemblies Defined by Multiple Supramolecular Interactions.
Authors: Long Li / Zhen Li / Ziying Wang / Shuyu Chen / Rongying Liu / Xuyang Xu / Zhi Zhang / Linfei Ye / Yu Ding / Quan Luo / Sheng Cao / Lei Zhang / Anne Imberty / Guosong Chen /
Abstract: Precise protein assemblies not only constitute a series of living machineries but also provide an advanced class of biomaterials. Previously, we developed the inducing ligand strategy to generate ...Precise protein assemblies not only constitute a series of living machineries but also provide an advanced class of biomaterials. Previously, we developed the inducing ligand strategy to generate various fixed protein assemblies, without the formation of noncovalent interactions between proteins. Here, we demonstrated that controlling the symmetry and number of supramolecular interactions introduced on protein surfaces could direct the formation of unspecific interactions between proteins and induce various nanoscale assemblies, including coiling nanowires, nanotubes, and nanosheets, without manipulation of the protein's native surfaces. More importantly, these nanoscale assemblies could spontaneously evolve into more ordered architectures, crystals. We further showed that the transformation from the introduced supramolecular interactions to the interactions formed between proteins was crucial for pathway selection and outcomes of evolution. These findings reveal a transformation mechanism of protein self-assembly that has not been exploited before and may provide an approach to generate complex and transformable biomacromolecular self-assemblies.
History
DepositionFeb 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 1.2Jul 29, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
B: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
C: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,94521
Polymers87,0163
Non-polymers5,92918
Water8,503472
1
A: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9827
Polymers29,0051
Non-polymers1,9766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9827
Polymers29,0051
Non-polymers1,9766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9827
Polymers29,0051
Non-polymers1,9766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.494, 161.519, 54.137
Angle α, β, γ (deg.)90.000, 91.530, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 29005.451 Da / Num. of mol.: 3 / Mutation: R17A,R108A,R153A,R244A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S4TLR1
#2: Chemical
ChemComp-R3F / 2-[2-[2-[4-[[(2R,3S,4R,5S,6S)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-1,2,3-triazol-1-yl]ethoxy]ethoxy]ethyl 2-[3,6-bis(diethylamino)-9H-xanthen-9-yl]benzoate


Mass: 803.940 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C43H57N5O10 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 7.5
Details: 20 mM Tris-HCl, 100 mM of NaCl pH 7.5, Micro centrifuge tube sequentially put with RSL solution, pure buffer, ligand solution

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.61→80.76 Å / Num. obs: 94580 / % possible obs: 98 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Net I/σ(I): 15 / Num. measured all: 597512 / Scaling rejects: 1268
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.61-1.694.80.5964788135520.8320.2960.6622.796.7
5.08-80.766.80.0572104331160.9980.0240.0623299.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4csd

4csd


Resolution: 1.61→80.76 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.765 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 4739 5 %RANDOM
Rwork0.2178 ---
obs0.2194 89341 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.92 Å2 / Biso mean: 21.416 Å2 / Biso min: 8.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.09 Å2
2--0.05 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.61→80.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6087 0 420 472 6979
Biso mean--55.18 25.31 -
Num. residues----808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136721
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185612
X-RAY DIFFRACTIONr_angle_refined_deg1.961.7149235
X-RAY DIFFRACTIONr_angle_other_deg1.5851.65312984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2775801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15123.218261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3715793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5431515
X-RAY DIFFRACTIONr_chiral_restr0.0840.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.027475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021510
LS refinement shellResolution: 1.61→1.65 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.301 302 -
Rwork0.288 6371 -
obs--94.41 %
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)
10.51650.27590.11910.5740.22220.7408-0.08360.00970.03860.020.0576-0.02630.00350.07160.0260.02930.0089-0.00380.0479-0.01390.03237.9635-14.752466.1524
20.2132-0.2742-0.05060.70590.10631.0977-0.0449-0.0054-0.0891-0.0458-0.07030.1405-0.0122-0.05760.11520.040.01670.01440.049-0.02820.0611-10.3976-40.673439.4003
30.38740.2462-0.14571.4571-0.62711.0976-0.12620.01980.0027-0.0180.1240.182-0.007-0.00320.00220.0472-0.0041-0.00340.01430.02490.0635-10.709411.279639.6024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 401
2X-RAY DIFFRACTION2B1 - 401
3X-RAY DIFFRACTION3C2 - 401

+
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