[English] 日本語
Yorodumi
- PDB-5cil: Crystal Structure of non-neutralizing version of 4E10 (WDWD) with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cil
TitleCrystal Structure of non-neutralizing version of 4E10 (WDWD) with epitope bound
Components
  • FAB 4E10 HEAVY CHAIN
  • FAB 4E10 LIGHT CHAIN
  • Peptide from the MPER region of the ENV protein of HIV-1
KeywordsIMMUNE SYSTEM / BROADLY NEUTRALIZING ANTIBODY / RECOMBINANT FAB / ENV-PEPTIDE / HIV-1 / EPITOPE
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsCaaveiro, J.M.M. / Rujas, E. / Nieva, J.L. / Tsumoto, K.
Funding support United States, Japan, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI097051-01 United States
Japan Society for the Promotion of Science25249115 Japan
CitationJournal: J.Virol. / Year: 2015
Title: Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10
Authors: Rujas, E. / Gulzar, N. / Morante, K. / Tsumoto, K. / Scott, J.K. / Nieva, J.L. / Caaveiro, J.M.M.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Nov 8, 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
H: FAB 4E10 HEAVY CHAIN
L: FAB 4E10 LIGHT CHAIN
P: Peptide from the MPER region of the ENV protein of HIV-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1998
Polymers48,8853
Non-polymers3145
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-54 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.300, 44.890, 86.160
Angle α, β, γ (deg.)90.00, 114.53, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide Peptide from the MPER region of the ENV protein of HIV-1 /


Mass: 2187.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS

-
Antibody , 2 types, 2 molecules HL

#1: Antibody FAB 4E10 HEAVY CHAIN


Mass: 23590.473 Da / Num. of mol.: 1 / Mutation: W100D, W100(B)D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T7 Shuffle
#2: Antibody FAB 4E10 LIGHT CHAIN


Mass: 23106.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T7 Shuffle

-
Non-polymers , 4 types, 414 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.03 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 100mM TRIS-HCl, 200mM Ammonium acetate, 34%PEG 4,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→44.5 Å / Num. obs: 50189 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.9
Reflection shellResolution: 1.81→1.91 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.8 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WY7

4wy7


Resolution: 1.81→44.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.852 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18838 2007 4 %RANDOM
Rwork0.16306 ---
obs0.16408 48180 99.69 %-
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: 28.386 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20.78 Å2
2---1.3 Å20 Å2
3---1.12 Å2
Refinement stepCycle: 1 / Resolution: 1.81→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 0 18 409 3803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023593
X-RAY DIFFRACTIONr_bond_other_d0.0010.023318
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9514921
X-RAY DIFFRACTIONr_angle_other_deg0.8063.0027686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1755.021484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89824.138145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72515569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5051518
X-RAY DIFFRACTIONr_chiral_restr0.1020.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214130
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02819
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_it1.3841.7041826
X-RAY DIFFRACTIONr_mcbond_other1.3791.7011824
X-RAY DIFFRACTIONr_mcangle_it2.1452.5412286
X-RAY DIFFRACTIONr_mcangle_other2.1452.5422287
X-RAY DIFFRACTIONr_scbond_it2.0491.9431767
X-RAY DIFFRACTIONr_scbond_other2.0491.9441768
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2282.8132616
X-RAY DIFFRACTIONr_long_range_B_refined6.45415.2534181
X-RAY DIFFRACTIONr_long_range_B_other6.31114.4964001
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 139 -
Rwork0.243 3505 -
obs--99.16 %
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)
10.98660.02250.43851.02920.48841.58730.04610.0790.0541-0.0793-0.0557-0.0883-0.01280.02160.00960.01570.01590.02590.01790.0270.04818.78227.1445-4.7387
20.6846-0.2958-0.32240.85920.74082.02020.0415-0.0559-0.02580.0773-0.0137-0.0030.0766-0.0657-0.02790.0216-0.0130.00310.01940.02060.062919.5163-7.85275.2496
312.08412.2057-6.3040.7566-0.7310.6178-0.13830.834-0.3679-0.36120.103-0.15150.20510.00880.03530.37440.06170.05250.1888-0.02080.110320.7566-6.895-34.103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2 - 227
2X-RAY DIFFRACTION2L1 - 211
3X-RAY DIFFRACTION3P671 - 683

+
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