[English] 日本語
Yorodumi
- PDB-8fwf: Crystal structure of Apo form Fab235 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fwf
TitleCrystal structure of Apo form Fab235
Components
  • Fab235, heavy chain
  • Fab235, light chain
KeywordsIMMUNE SYSTEM / HIV / membrane proximal external region / MPER / vaccine
Function / homologyACETATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsTan, K. / Kim, M. / Reinherz, E.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145509 United States
CitationJournal: Nat Commun / Year: 2023
Title: Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility.
Authors: Tan, K. / Chen, J. / Kaku, Y. / Wang, Y. / Donius, L. / Khan, R.A. / Li, X. / Richter, H. / Seaman, M.S. / Walz, T. / Hwang, W. / Reinherz, E.L. / Kim, M.
History
DepositionJan 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Fab235, light chain
H: Fab235, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,57928
Polymers48,4712
Non-polymers2,10726
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-146 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.755, 120.755, 86.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11H-519-

HOH

-
Components

-
Antibody , 2 types, 2 molecules LH

#1: Antibody Fab235, light chain


Mass: 24203.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): 293 F cells
#2: Antibody Fab235, heavy chain


Mass: 24267.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): 293 F cells

-
Non-polymers , 7 types, 267 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0M Ammonium Sulphate, 0.1M HEPES:NaOH, 2%(v/v) PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2022
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 46067 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 25.75 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.065 / Rrim(I) all: 0.142 / Χ2: 1.42 / Net I/σ(I): 15.5
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 2312 / CC1/2: 0.505 / CC star: 0.819 / Rpim(I) all: 0.532 / Χ2: 0.734 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→49.59 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2057 2272 4.94 %
Rwork0.1705 43708 -
obs0.1722 45980 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.48 Å2
Refinement stepCycle: LAST / Resolution: 1.94→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 119 241 3753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013656
X-RAY DIFFRACTIONf_angle_d1.04194976
X-RAY DIFFRACTIONf_chiral_restr0.0692546
X-RAY DIFFRACTIONf_plane_restr0.012629
X-RAY DIFFRACTIONf_dihedral_angle_d9.2407523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.26671380.22652576X-RAY DIFFRACTION92
1.99-2.030.25541230.20452766X-RAY DIFFRACTION98.63
2.03-2.080.21281380.19882765X-RAY DIFFRACTION98.14
2.08-2.140.2461580.18652701X-RAY DIFFRACTION98.01
2.14-2.20.20711470.18272738X-RAY DIFFRACTION97.83
2.2-2.270.22961420.17742739X-RAY DIFFRACTION97.56
2.27-2.350.21171390.1772738X-RAY DIFFRACTION97.36
2.35-2.450.2311410.18052731X-RAY DIFFRACTION97.13
2.45-2.560.25131420.18762743X-RAY DIFFRACTION96.78
2.56-2.70.24661210.19362734X-RAY DIFFRACTION96.55
2.7-2.860.2271490.18312746X-RAY DIFFRACTION96.66
2.86-3.090.21741650.17932726X-RAY DIFFRACTION96.85
3.09-3.40.19461340.17072759X-RAY DIFFRACTION96.69
3.4-3.890.18921410.1542750X-RAY DIFFRACTION95.13
3.89-4.90.15711480.13282718X-RAY DIFFRACTION93.45
4.9-49.590.1931460.16682778X-RAY DIFFRACTION90.5
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)
12.67253150130.206508193840.5010065828211.96057445017-0.4400082836992.51293584659-0.101462835546-0.05678137224020.475933776470.11365958448-0.00737467659399-0.0991482861368-0.3849024606260.02610294591940.09515736132150.246612473653-0.002220433305690.01912834081970.120947624573-0.02068891720660.2408630833132.6753784469535.99437000312.80049356682
23.28199888941-0.01104559186541.735374771450.08407866816630.1351106179081.13160438437-0.11411440649-0.1631564644410.3199944656450.1036271838280.0470064449045-0.080812803486-0.1727518661990.01264570147840.04014515258860.26275185153-0.03993211524710.00609048779440.195005377693-0.04752039396550.24330003284517.975141494827.896396719811.780699817
32.78153552371-1.148493165910.4952411213765.723382789910.3489975247571.70241485823-0.074243947430.1656861122040.0409761640728-0.2293999538470.121746630155-0.427546143157-0.05143359029340.30295664429-0.0357914302330.231996496674-0.0884655424759-0.001419830348970.303710408577-0.08601785084690.25206980995538.520531170721.889266136716.34407494
42.25795999419-1.432832128350.340948268553.13760902901-0.08039986233490.8625800295760.0226987698288-0.3107472594470.3536376966230.3188291995250.0562670174308-0.39110576218-0.09247749612810.0317473665721-0.08477698623010.198968662319-0.02010225889020.03973762302320.211461158019-0.03666254580270.1613473614730.24888662543215.221243890914.709409222
51.73815675361-0.3608324737460.7495393376981.98989914514-0.3141219999431.088198943260.0414910791623-0.06766275870740.08969802201860.1134716788460.008767378113570.0604532483093-0.0839685007299-0.123023590096-0.05103877832390.159237320009-0.005617210529920.05096237724580.14895559899-0.02347918405850.108571467978-3.8389542924415.85694879449.1732974712
60.9586690942090.6049966856790.7967190779460.9757221231660.2934082574620.7060850438760.111625015992-0.3464429667430.3558619827330.248898188695-0.2874476200920.1834806236450.100679368695-0.1847168839370.1545026593040.260643718489-0.0611893207425-0.007756704950550.338012188951-0.1322657332410.27958410167227.155894620418.048893328224.8813349084
74.321086976272.483617644672.368551013545.080248969952.905251152923.454756795450.593906397125-0.710856580362-0.08349039452110.894341683197-0.45040366617-0.2365527773420.395984861008-0.201461086051-0.02007348073130.469853164693-0.1774060699960.05010845997750.536691051837-0.1128518529060.30092652089326.23283687717.003050171333.9447948892
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'L' and (resid 1 through 81 )LA1 - 811 - 81
22chain 'L' and (resid 82 through 134 )LA82 - 13482 - 134
33chain 'L' and (resid 135 through 220 )LA135 - 220135 - 220
44chain 'H' and (resid 1 through 44 )HB1 - 441 - 44
55chain 'H' and (resid 45 through 121 )HB45 - 12145 - 121
66chain 'H' and (resid 122 through 198 )HB122 - 198122 - 198
77chain 'H' and (resid 199 through 226 )HB199 - 226199 - 226

+
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