[English] 日本語
Yorodumi
- PDB-7v5n: Crystal structure of Fab fragment of bevacizumab bound to DNA aptamer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v5n
TitleCrystal structure of Fab fragment of bevacizumab bound to DNA aptamer
Components
  • (bevacizumab fab ...) x 2
  • DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3')
KeywordsIMMUNE SYSTEM/DNA / antibody / DNA complex / DNA BINDING PROTEIN / IMMUNE SYSTEM-DNA complex
Function / homologyIMIDAZOLE / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHishiki, A. / Tong, J. / Todoroki, K. / Hashimoto, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H03360 Japan
CitationJournal: Biosens.Bioelectron. / Year: 2022
Title: Development of a DNA aptamer that binds to the complementarity-determining region of therapeutic monoclonal antibody and affinity improvement induced by pH-change for sensitive detection.
Authors: Saito, T. / Shimizu, Y. / Tsukakoshi, K. / Abe, K. / Lee, J. / Ueno, K. / Asano, R. / Jones, B.V. / Yamada, T. / Nakano, T. / Tong, J. / Hishiki, A. / Hara, K. / Hashimoto, H. / Sode, K. / ...Authors: Saito, T. / Shimizu, Y. / Tsukakoshi, K. / Abe, K. / Lee, J. / Ueno, K. / Asano, R. / Jones, B.V. / Yamada, T. / Nakano, T. / Tong, J. / Hishiki, A. / Hara, K. / Hashimoto, H. / Sode, K. / Toyo'oka, T. / Todoroki, K. / Ikebukuro, K.
History
DepositionAug 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: bevacizumab fab light chain
B: bevacizumab fab heavy chain
D: DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3')
E: bevacizumab fab light chain
F: bevacizumab fab heavy chain
G: DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,35531
Polymers111,6536
Non-polymers1,70225
Water11,728651
1
E: bevacizumab fab light chain
F: bevacizumab fab heavy chain
G: DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,64615
Polymers55,8263
Non-polymers82012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-36 kcal/mol
Surface area21770 Å2
MethodPISA
2
A: bevacizumab fab light chain
B: bevacizumab fab heavy chain
D: DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,70816
Polymers55,8263
Non-polymers88213
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-54 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.543, 130.599, 90.244
Angle α, β, γ (deg.)90.00, 103.59, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
DNA chain , 1 types, 2 molecules DG

#3: DNA chain DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3')


Mass: 7463.784 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA aptamer / Source: (synth.) synthetic construct (others)

-
Antibody , 2 types, 4 molecules AEBF

#1: Antibody bevacizumab fab light chain


Mass: 23471.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody bevacizumab fab heavy chain


Mass: 24890.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

-
Non-polymers , 4 types, 676 molecules

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


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 104111 / % possible obs: 99.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.6
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.511 / Num. unique obs: 15208

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bj1

1bj1


Resolution: 1.7→19.71 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.389 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21002 5050 4.9 %RANDOM
Rwork0.178 ---
obs0.17952 99026 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.467 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6610 990 106 651 8357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0127984
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.56811049
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8645858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03423.31290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.354151043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3131520
X-RAY DIFFRACTIONr_chiral_restr0.0790.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025690
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2723.013447
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0774.5094300
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6643.0494537
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.89439.37512370
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 398 -
Rwork0.27 7235 -
obs--99.86 %

+
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