[English] 日本語
Yorodumi
- PDB-8vu4: Structure of FabS1CE4-EPR-1, an elbow-locked high affinity antibo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vu4
TitleStructure of FabS1CE4-EPR-1, an elbow-locked high affinity antibody for the erythropoeitin receptor
Components(S1CE4 VARIANT OF FAB-EPR-1 ...) x 2
KeywordsIMMUNE SYSTEM / proliferation / engineered antibody / high-affinity binding / enhanced crystallization
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSinger, A.U. / Bruce, H.A. / Pavlenco, A. / Ploder, L. / Luu, G. / Blazer, L. / Adams, J.J. / Sidhu, S.S.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-159640 Canada
Other private United States
CitationJournal: Protein Sci. / Year: 2024
Title: Antigen-binding fragments with improved crystal lattice packing and enhanced conformational flexibility at the elbow region as crystallization chaperones.
Authors: Bruce, H.A. / Singer, A.U. / Blazer, L.L. / Luu, K. / Ploder, L. / Pavlenco, A. / Kurinov, I. / Adams, J.J. / Sidhu, S.S.
History
DepositionJan 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: S1CE4 VARIANT OF FAB-EPR-1 heavy chain
C: S1CE4 VARIANT OF FAB-EPR-1 light chain
A: S1CE4 VARIANT OF FAB-EPR-1 heavy chain
G: S1CE4 VARIANT OF FAB-EPR-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,32731
Polymers94,3674
Non-polymers96027
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12150 Å2
ΔGint-254 kcal/mol
Surface area36220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.863, 55.893, 87.016
Angle α, β, γ (deg.)80.050, 89.910, 82.700
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Antibody , 2 types, 4 molecules BACG

#1: Antibody S1CE4 VARIANT OF FAB-EPR-1 heavy chain


Mass: 24134.004 Da / Num. of mol.: 2 / Mutation: K131Q and F160W
Source method: isolated from a genetically manipulated source
Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND COMPND 7 SELECTED BY PHAGE DISPLAY. FABS UTILIZE IMGT (LECLERC ET AL., DEV COMPND 8 COMP IMMUNOL. 2003 JAN;27(1):55-77) NUMBERING
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PSCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody S1CE4 VARIANT OF FAB-EPR-1 light chain


Mass: 23049.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND COMPND 7 SELECTED BY PHAGE DISPLAY. FABS UTILIZE IMGT (LECLERC ET AL., DEV COMPND 8 COMP IMMUNOL. 2003 JAN;27(1):55-77) NUMBERING
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PSCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

-
Non-polymers , 5 types, 228 molecules

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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M BICINE 9.0, 10% PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.27→85.69 Å / Num. obs: 43559 / % possible obs: 91.5 % / Redundancy: 2 % / Biso Wilson estimate: 44.79 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.115 / Rrim(I) all: 0.162 / Net I/σ(I): 8.3
Reflection shellResolution: 2.27→2.34 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4024 / CC1/2: 0.508 / Rpim(I) all: 0.479 / Rrim(I) all: 0.677 / % possible all: 91.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→55.4 Å / SU ML: 0.3678 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 29.9726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2516 1899 4.85 %
Rwork0.2084 37275 -
obs0.2105 39174 91.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.27 Å2
Refinement stepCycle: LAST / Resolution: 2.35→55.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6385 0 45 201 6631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816608
X-RAY DIFFRACTIONf_angle_d1.06349002
X-RAY DIFFRACTIONf_chiral_restr0.05921023
X-RAY DIFFRACTIONf_plane_restr0.00951153
X-RAY DIFFRACTIONf_dihedral_angle_d16.94672319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.34761370.29092705X-RAY DIFFRACTION92.97
2.41-2.470.29631500.26842712X-RAY DIFFRACTION93.16
2.47-2.550.31781130.26142743X-RAY DIFFRACTION92.76
2.55-2.630.33021150.25362682X-RAY DIFFRACTION92.13
2.63-2.720.31051570.25272632X-RAY DIFFRACTION91.2
2.72-2.830.31971460.24142552X-RAY DIFFRACTION89.01
2.83-2.960.30141260.23372547X-RAY DIFFRACTION86
2.96-3.120.29791390.23362731X-RAY DIFFRACTION94.13
3.12-3.310.32471240.24252713X-RAY DIFFRACTION93.48
3.31-3.570.24471260.20612700X-RAY DIFFRACTION92.69
3.57-3.930.23971270.20132647X-RAY DIFFRACTION90.51
3.93-4.490.20731330.16242502X-RAY DIFFRACTION86.31
4.5-5.660.18331680.16942781X-RAY DIFFRACTION95.5
5.66-55.40.24161380.1972628X-RAY DIFFRACTION90.84
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)
13.05916500516-0.635908031347-0.6418533915045.06287802665-1.295625099496.067552747470.00608044129967-0.5113998815240.1543186229270.9081856363270.4192915206150.607011773963-0.667981015062-0.845715389348-0.1819812822630.5448002727230.1003663378280.03535244487340.580764787679-0.04565567984980.463826631541-32.33519.5825.714
22.73228144125-0.814520145278-0.1546071660274.54301260443-0.3746641382424.879292246680.0279663271277-0.4186711078040.2375752390160.6299691895040.0788644111034-0.0136624748576-0.614240845711-0.185945743761-0.1149440296710.5129387437130.0584806063163-0.0640373467260.43103818195-0.05539821268910.372009483932-24.92421.2685.837
33.575910845660.0456144362246-1.467056293612.37944582389-0.09784034338922.09781632098-0.03011406184890.0002907140137520.025414201095-0.0987252291678-0.0987794907891-0.1556455291760.08562458613880.1196767289350.1177035851350.2638551876110.0494843989138-0.04064983783660.252449398538-0.006391544142480.349922752974-3.80925.674-24.441
43.05609450001-1.81313830212-2.058866477845.91612738939-0.01523111799872.328357780820.0280622660645-0.3144910470050.171143086670.455254088366-0.0314751277777-0.40391046899-0.007143789113990.3610392645760.002150266981140.4392061415320.0310505077353-0.1416494269050.579000439897-0.008712426700110.339621027843-12.0783.97910.69
52.477917701660.9932820655792.143414040654.999353329883.109728194175.21532914049-0.1534234812220.1100562984080.0846174510369-0.04397761146460.05507493399650.0590109858046-0.1997908584470.2014332244170.08744325491550.1684263668860.01119321193530.07762316375250.3455938051960.042447772180.251507642309-21.258-1.563-10.5
63.41615009141-1.841652586310.642592883594.839202304020.2769539239316.95070132699-0.009660954273860.06667257542050.0821321879344-0.2134909939840.0118837401819-0.26266585601-0.150304158305-0.159508737596-0.01397408552010.268012498423-0.004376106213710.02032975774140.2130799529770.01945018435260.326461149656-20.808-8.282-23.57
74.52193271173-1.56169950538-0.07889963138472.955864152050.4024153120574.422167052330.2881681371050.7692797467990.201414540282-1.01016063341-0.2721761220420.412023226333-0.497137472486-0.575463081502-0.06740158607010.6527979503440.131327703637-0.1465507277680.6001049171440.005958298431840.4387968732-28.11321.097-47
86.166961189-1.58084020573-0.6259437582394.047796802640.2171825812715.778713213560.1976886386020.4716525865270.266952098401-0.83589758776-0.09131361117630.0441444412713-0.310873856934-0.318672562781-0.03575228281180.550493247330.00843568774971-0.0922380072930.389215729153-0.01330544842370.38955027224-24.68720.055-44.769
93.01120968763-0.2577273110330.02297590443193.72259419243-1.027910748032.23322915695-0.128581151846-0.106745705778-0.01304130654160.07688388309720.03880773225890.108917224680.0232329254258-0.07896392360410.08663991239210.2837081987750.049535573449-0.03076292706490.26677397259-0.01346620791470.279316312001-34.623-1.536-16.482
103.00980725656-0.471945374041.449791523643.128943649061.075592074494.763579288630.08789033365310.729046653068-0.332915569594-0.542282242495-0.06780161824960.05170610290650.3126417393450.0582718738933-0.02983409812440.592121389020.0262337750984-0.009479423593990.550756359762-0.09096355235360.328703583696-11.3164.002-50.022
114.93167596794-2.16127259134-0.3464404095125.031991930571.096134435874.20793382311-0.0860845259558-0.486842644423-0.1331150124620.1928931358110.03155566070030.079400062836-0.104045957054-0.2553151944230.04563283997160.228635001210.0105558167857-0.0232010702850.3100730005450.01645126412530.2877824630621.1812.82-16.628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:38 )B1 - 38
2X-RAY DIFFRACTION2( CHAIN B AND RESID 39:124 )B39 - 124
3X-RAY DIFFRACTION3( CHAIN B AND RESID 125:228 )B125 - 228
4X-RAY DIFFRACTION4( CHAIN C AND RESID 1:107 )C1 - 107
5X-RAY DIFFRACTION5( CHAIN C AND RESID 108:148 )C108 - 148
6X-RAY DIFFRACTION6( CHAIN C AND RESID 149:232 )C149 - 232
7X-RAY DIFFRACTION7( CHAIN A AND RESID 2:84 )A2 - 84
8X-RAY DIFFRACTION8( CHAIN A AND RESID 85:124 )A85 - 124
9X-RAY DIFFRACTION9( CHAIN A AND RESID 125:229 )A125 - 229
10X-RAY DIFFRACTION10( CHAIN G AND RESID 2:133 )G2 - 133
11X-RAY DIFFRACTION11( CHAIN G AND RESID 134:231 )G134 - 231

+
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