[English] 日本語
Yorodumi
- PDB-7lfb: Fab 7D6 bound to ApoL1 NTD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lfb
TitleFab 7D6 bound to ApoL1 NTD
Components
  • Apolipoprotein L1
  • Fab 7D6 heavy chain
  • Fab 7D6 light chain
KeywordsIMMUNE SYSTEM / Complex
Function / homology
Function and homology information


lipoprotein metabolic process / very-low-density lipoprotein particle / high-density lipoprotein particle / lipid transport / chloride channel activity / cytolysis by host of symbiont cells / Scavenging of heme from plasma / chloride transmembrane transport / cholesterol metabolic process / Post-translational protein phosphorylation ...lipoprotein metabolic process / very-low-density lipoprotein particle / high-density lipoprotein particle / lipid transport / chloride channel activity / cytolysis by host of symbiont cells / Scavenging of heme from plasma / chloride transmembrane transport / cholesterol metabolic process / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood microparticle / endoplasmic reticulum lumen / innate immune response / lipid binding / extracellular space / extracellular region / membrane
Similarity search - Function
Apolipoprotein L / Apolipoprotein L
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.913 Å
AuthorsUltsch, M. / Kirchhofer, D.
CitationJournal: Commun Biol / Year: 2021
Title: Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif.
Authors: Ultsch, M. / Holliday, M.J. / Gerhardy, S. / Moran, P. / Scales, S.J. / Gupta, N. / Oltrabella, F. / Chiu, C. / Fairbrother, W. / Eigenbrot, C. / Kirchhofer, D.
History
DepositionJan 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 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 7D6 heavy chain
L: Fab 7D6 light chain
X: Apolipoprotein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2378
Polymers62,6663
Non-polymers5725
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-50 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.238, 60.262, 124.216
Angle α, β, γ (deg.)90.000, 111.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-523-

HOH

21X-226-

HOH

-
Components

-
Protein , 1 types, 1 molecules X

#3: Protein Apolipoprotein L1 / / Apolipoprotein L / ApoL / Apolipoprotein L-I / ApoL-I


Mass: 15289.139 Da / Num. of mol.: 1 / Fragment: residues 61-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOL1, APOL / Production host: Baculoviridae sp. (virus) / References: UniProt: O14791

-
Antibody , 2 types, 2 molecules HL

#1: Antibody Fab 7D6 heavy chain


Mass: 24050.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: AEP1 / Production host: Escherichia coli (E. coli) / Strain (production host): 64B4
#2: Antibody Fab 7D6 light chain


Mass: 23325.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: AEP1 / Production host: Escherichia coli (E. coli) / Strain (production host): 64B4

-
Non-polymers , 4 types, 411 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.61 Å3/Da / Density % sol: 52.92 % / Description: blocks
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15%(w/v) PEG 4000, 0.15M Ammonium sulfate, 0.1M MES pH 6
PH range: 6.0 - 7.0

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→49.628 Å / Num. obs: 51638 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.047 / Rrim(I) all: 0.068 / Net I/σ(I): 11.4
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3305 / CC1/2: 0.81 / Rpim(I) all: 0.339 / Rrim(I) all: 0.584 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVD

1fvd


Resolution: 1.913→49.628 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 2504 5.06 %
Rwork0.1677 46952 -
obs0.1692 49456 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.35 Å2 / Biso mean: 43.0132 Å2 / Biso min: 14.33 Å2
Refinement stepCycle: final / Resolution: 1.913→49.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 42 406 4439
Biso mean--58.74 43.38 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064161
X-RAY DIFFRACTIONf_angle_d0.9615643
X-RAY DIFFRACTIONf_chiral_restr0.038621
X-RAY DIFFRACTIONf_plane_restr0.004725
X-RAY DIFFRACTIONf_dihedral_angle_d14.3161514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.913-1.94970.32561460.27082624100
1.9497-1.98950.2681390.232612100
1.9895-2.03280.22291400.21072612100
2.0328-2.080.24331550.1952640100
2.08-2.13210.2471620.18822602100
2.1321-2.18970.23251510.18372593100
2.1897-2.25410.20081350.18662660100
2.2541-2.32690.23161470.18261599
2.3269-2.41010.23541230.17832641100
2.4101-2.50650.1941380.18012618100
2.5065-2.62060.23171180.1787264899
2.6206-2.75880.24171280.1795263299
2.7588-2.93160.20561450.1725261499
2.9316-3.15790.19761330.1765258598
3.1579-3.47560.21091480.1625253496
3.4756-3.97840.20311250.1556253395
3.9784-5.01160.12251330.1316252594
5.0116-49.6280.16581380.154266497
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)
10.90940.0750.12331.09380.02411.4427-0.00550.1689-0.0234-0.10790.001-0.3138-0.14910.4088-0.0030.1698-0.01380.01790.2496-0.04030.313611.9392-1.137945.0917
21.30110.2086-0.29451.1365-0.00811.1004-0.0090.1235-0.0007-0.0868-0.0032-0.0529-0.0134-0.0140.01490.15850.0061-0.01140.1521-0.02950.2202-5.49961.022248.2706
30.6933-0.0074-0.06511.02190.12880.6291-0.01670.37190.1274-0.2401-0.07950.1677-0.4111-0.19340.05510.76620.00410.15870.9003-0.00970.2357-3.84955.9480.8943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'H' and resid 1 through 224)H1 - 224
2X-RAY DIFFRACTION2(chain 'L' and resid 1 through 214)L1 - 214
3X-RAY DIFFRACTION3(chain 'X' and resid 91 through 170)X91 - 170

+
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