[English] 日本語
Yorodumi
- PDB-8zpu: Crystal structure of the anti-phosphorylated peptide C7 scFv anti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zpu
TitleCrystal structure of the anti-phosphorylated peptide C7 scFv antibody with peptide bound
Components
  • PHE-PRO-GLN-PHE-SEP-TYR-SER
  • scFv
KeywordsIMMUNE SYSTEM / phosphorylated peptide / antibody
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCaaveiro, J.M.M. / Kawade, R. / Tsumoto, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K06962 Japan
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Unveiling the structural mechanisms behind high affinity and selectivity in phosphorylated epitope-specific rabbit antibodies.
Authors: Kasahara, K. / Kawade, R. / Nakakido, M. / Matsunaga, R. / Akiba, H. / Entzminger, K.C. / Maruyama, T. / Okumura, S.C.J. / Caaveiro, J.M.M. / Kuroda, D. / Tsumoto, K.
History
DepositionMay 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation
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: scFv
C: PHE-PRO-GLN-PHE-SEP-TYR-SER
B: scFv
D: PHE-PRO-GLN-PHE-SEP-TYR-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,21312
Polymers56,5664
Non-polymers6478
Water25214
1
A: scFv
C: PHE-PRO-GLN-PHE-SEP-TYR-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6076
Polymers28,2832
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-54 kcal/mol
Surface area10350 Å2
MethodPISA
2
B: scFv
D: PHE-PRO-GLN-PHE-SEP-TYR-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6076
Polymers28,2832
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-46 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.610, 126.610, 82.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-304-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 248 / Label seq-ID: 1 - 248

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Antibody scFv


Mass: 26777.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli BL21 (bacteria)
#2: Protein/peptide PHE-PRO-GLN-PHE-SEP-TYR-SER


Mass: 1505.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 30% Polyethylene glycol 4000, 20 mM Tris HCl, 20 mM NaCl, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→21.1 Å / Num. obs: 19037 / % possible obs: 99.8 % / Redundancy: 11.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.055 / Net I/σ(I): 12.8
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2756 / CC1/2: 0.807 / Rpim(I) all: 0.321

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOSFLM7.4.0data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→21.1 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.785 / SU B: 44.111 / SU ML: 0.423 / Cross valid method: THROUGHOUT / ESU R: 1.079 / ESU R Free: 0.464
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3452 1971 10.364 %
Rwork0.3044 17046 -
all0.309 --
obs-19017 99.691 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.864 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å2-0 Å2
2---0.24 Å2-0 Å2
3---0.778 Å2
Refinement stepCycle: LAST / Resolution: 2.8→21.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 0 32 14 3648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123711
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163304
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.7765065
X-RAY DIFFRACTIONr_angle_other_deg0.4911.7257605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4565473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.979516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37110545
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.46710147
X-RAY DIFFRACTIONr_chiral_restr0.0640.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02882
X-RAY DIFFRACTIONr_nbd_refined0.1860.2574
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.23026
X-RAY DIFFRACTIONr_nbtor_refined0.180.21785
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21972
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2103
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1190.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.218
X-RAY DIFFRACTIONr_nbd_other0.2410.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.26
X-RAY DIFFRACTIONr_mcbond_it1.9192.7911910
X-RAY DIFFRACTIONr_mcbond_other1.9182.7911910
X-RAY DIFFRACTIONr_mcangle_it3.1715.0032377
X-RAY DIFFRACTIONr_mcangle_other3.1715.0042378
X-RAY DIFFRACTIONr_scbond_it2.0923.0171801
X-RAY DIFFRACTIONr_scbond_other1.9762.9811778
X-RAY DIFFRACTIONr_scangle_it3.3445.4852688
X-RAY DIFFRACTIONr_scangle_other3.2645.4262653
X-RAY DIFFRACTIONr_lrange_it5.63528.4583857
X-RAY DIFFRACTIONr_lrange_other5.63528.463858
X-RAY DIFFRACTIONr_ncsr_local_group_10.0850.056941
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.084710.0501
12AX-RAY DIFFRACTIONLocal ncs0.084710.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8720.4041450.3171211X-RAY DIFFRACTION99.8527
2.872-2.9490.3771440.3191204X-RAY DIFFRACTION100
2.949-3.0320.429930.2981187X-RAY DIFFRACTION100
3.032-3.1240.3611440.3141109X-RAY DIFFRACTION100
3.124-3.2240.3481130.3141132X-RAY DIFFRACTION100
3.224-3.3340.3611510.3071042X-RAY DIFFRACTION100
3.334-3.4570.3581150.2991026X-RAY DIFFRACTION100
3.457-3.5940.3241090.2961027X-RAY DIFFRACTION100
3.594-3.7490.3721340.319911X-RAY DIFFRACTION100
3.749-3.9260.3631170.317915X-RAY DIFFRACTION100
3.926-4.130.3661080.294847X-RAY DIFFRACTION100
4.13-4.370.333870.289848X-RAY DIFFRACTION100
4.37-4.6580.367800.287804X-RAY DIFFRACTION100
4.658-5.0110.243960.287717X-RAY DIFFRACTION100
5.011-5.4580.308620.282702X-RAY DIFFRACTION100
5.458-6.0520.309840.278617X-RAY DIFFRACTION100
6.052-6.8940.358670.319566X-RAY DIFFRACTION100
6.894-8.2270.341460.316491X-RAY DIFFRACTION100
8.227-10.8410.255460.342403X-RAY DIFFRACTION100
10.841-21.10.522300.378287X-RAY DIFFRACTION100
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)
12.64651.41230.09192.257-0.24852.4907-0.0421-0.16070.24090.3248-0.06220.037-0.0354-0.08690.10430.14420.0770.02390.09040.03450.066250.4344-19.0851-2.5552
24.6832-0.52592.083915.9471-2.38243.7874-0.0711-0.615-0.033-0.2348-0.0828-0.382-0.2051-0.32960.15390.24110.0044-0.02770.177-0.03720.20354.234-10.979313.8784
33.14421.3415-0.02372.58990.09241.9846-0.09120.19870.1363-0.2928-0.0070.21150.0527-0.13520.09820.07710.00640.00850.0257-0.00080.042253.9355-17.3903-35.5603
416.156-4.2357-2.66147.509-1.44871.1622-0.32340.51890.2015-0.39730.37890.09130.1911-0.2604-0.05550.2861-0.0255-0.09980.14540.01180.212145.3363-17.2336-52.9331
Refinement TLS groupSelection: 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