[English] 日本語
Yorodumi
- PDB-4xbg: Crystal structure of human 4E10 Fab in complex with phosphatidic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xbg
TitleCrystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0 PA): 2.73 A resolution
Components
  • 4E10 Fab heavy chain
  • 4E10 Fab light chain
KeywordsIMMUNE SYSTEM / human anti gp41 HIV-1 4E10 Fab / membrane lipid / phosphatidic acid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / PHOSPHATE ION / Unknown ligand
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsIrimia, A. / Stanfield, R.L. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI084817 United States
CitationJournal: Immunity / Year: 2016
Title: Crystallographic Identification of Lipid as an Integral Component of the Epitope of HIV Broadly Neutralizing Antibody 4E10.
Authors: Irimia, A. / Sarkar, A. / Stanfield, R.L. / Wilson, I.A.
History
DepositionDec 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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
L: 4E10 Fab light chain
H: 4E10 Fab heavy chain
B: 4E10 Fab light chain
A: 4E10 Fab heavy chain
D: 4E10 Fab light chain
C: 4E10 Fab heavy chain
F: 4E10 Fab light chain
E: 4E10 Fab heavy chain
I: 4E10 Fab light chain
G: 4E10 Fab heavy chain
K: 4E10 Fab light chain
J: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,12627
Polymers285,45712
Non-polymers1,66915
Water8,899494
1
L: 4E10 Fab light chain
H: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9444
Polymers47,5762
Non-polymers3682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-17 kcal/mol
Surface area19980 Å2
MethodPISA
2
B: 4E10 Fab light chain
A: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4977
Polymers47,5762
Non-polymers9215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-16 kcal/mol
Surface area20220 Å2
MethodPISA
3
D: 4E10 Fab light chain
C: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6714
Polymers47,5762
Non-polymers952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-26 kcal/mol
Surface area19500 Å2
MethodPISA
4
F: 4E10 Fab light chain
E: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6714
Polymers47,5762
Non-polymers952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-30 kcal/mol
Surface area19440 Å2
MethodPISA
5
I: 4E10 Fab light chain
G: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6714
Polymers47,5762
Non-polymers952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-22 kcal/mol
Surface area19260 Å2
MethodPISA
6
K: 4E10 Fab light chain
J: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6714
Polymers47,5762
Non-polymers952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-23 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.560, 149.560, 470.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

-
Antibody , 2 types, 12 molecules LBDFIKHACEGJ

#1: Antibody
4E10 Fab light chain


Mass: 23395.850 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)
#2: Antibody
4E10 Fab heavy chain


Mass: 24180.250 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)

-
Non-polymers , 5 types, 509 molecules

#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 6 / Source method: obtained synthetically
#4: Chemical ChemComp-44E / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate


Mass: 368.360 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H29O8P / Comment: phospholipid*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Nonpolymer detailsSIX UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ...SIX UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ENVIRONMENTS, THE COMPOUNDS MAY BE FRAGMENTS OF POLYETHYLENE GLYCOL 3350 OR LIPID TAIL FRAGMENTS OF 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHATE. THE DATA ARE INSUFFICIENT TO DISTINGUISH BETWEEN THE TWO COMPOUNDS AND THE TRUE IDENTITY OF THE LIGAND IS UNKNOWN.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Reservoir: 0.2 M potassium formate, 35% PEG 3350 / PH range: 6.5-7.0

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2013
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111), non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.73→39.241 Å / Num. obs: 81191 / % possible obs: 97.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 46.1 Å2 / Rsym value: 0.102 / Net I/σ(I): 14.8
Reflection shellResolution: 2.73→2.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FX7

2fx7


Resolution: 2.73→39.241 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 4057 5 %Random selection
Rwork0.2022 ---
obs0.2044 81170 97.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.73→39.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19437 0 180 494 20111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320287
X-RAY DIFFRACTIONf_angle_d0.82327613
X-RAY DIFFRACTIONf_dihedral_angle_d13.0047221
X-RAY DIFFRACTIONf_chiral_restr0.0323144
X-RAY DIFFRACTIONf_plane_restr0.0053562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.76610.38911360.30532593X-RAY DIFFRACTION96
2.7661-2.79980.31591380.28852624X-RAY DIFFRACTION99
2.7998-2.83530.37271400.28362660X-RAY DIFFRACTION100
2.8353-2.87260.38981420.27972684X-RAY DIFFRACTION100
2.8726-2.91190.33171390.26892633X-RAY DIFFRACTION99
2.9119-2.95350.31861390.2652643X-RAY DIFFRACTION98
2.9535-2.99760.32791380.28012628X-RAY DIFFRACTION98
2.9976-3.04440.32311370.26412616X-RAY DIFFRACTION97
3.0444-3.09430.28431390.24962614X-RAY DIFFRACTION99
3.0943-3.14760.29431380.23712644X-RAY DIFFRACTION99
3.1476-3.20480.24911410.23552658X-RAY DIFFRACTION99
3.2048-3.26640.32151390.23172660X-RAY DIFFRACTION99
3.2664-3.33310.32641400.23122659X-RAY DIFFRACTION99
3.3331-3.40550.25291400.21872674X-RAY DIFFRACTION99
3.4055-3.48470.26731380.21212614X-RAY DIFFRACTION98
3.4847-3.57180.25151400.20642662X-RAY DIFFRACTION98
3.5718-3.66830.29951380.21072593X-RAY DIFFRACTION96
3.6683-3.77610.27281350.21282591X-RAY DIFFRACTION96
3.7761-3.89790.23151390.19492635X-RAY DIFFRACTION97
3.8979-4.03710.23231420.18842684X-RAY DIFFRACTION98
4.0371-4.19850.21041390.17162652X-RAY DIFFRACTION98
4.1985-4.38940.18461420.15382692X-RAY DIFFRACTION98
4.3894-4.62050.17881410.15252683X-RAY DIFFRACTION98
4.6205-4.90940.18661370.15392619X-RAY DIFFRACTION95
4.9094-5.28770.21161430.15732698X-RAY DIFFRACTION97
5.2877-5.81830.20111410.17072698X-RAY DIFFRACTION97
5.8183-6.65660.21861450.17742726X-RAY DIFFRACTION97
6.6566-8.37320.21331430.19222731X-RAY DIFFRACTION95
8.3732-39.24510.20791480.19532845X-RAY DIFFRACTION93

+
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