[English] 日本語
Yorodumi
- PDB-7lfa: Fab 3B6 bound to ApoL1 NTD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lfa
TitleFab 3B6 bound to ApoL1 NTD
Components
  • Apolipoprotein L1
  • Fab 3B6 heavy chain
  • Fab 3B6 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: 1.857 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 15, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apolipoprotein L1
B: Fab 3B6 heavy chain
C: Apolipoprotein L1
D: Fab 3B6 light chain
H: Fab 3B6 heavy chain
L: Fab 3B6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,03910
Polymers123,7846
Non-polymers2554
Water6,954386
1
A: Apolipoprotein L1
B: Fab 3B6 heavy chain
D: Fab 3B6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0205
Polymers61,8923
Non-polymers1282
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-39 kcal/mol
Surface area24710 Å2
MethodPISA
2
C: Apolipoprotein L1
H: Fab 3B6 heavy chain
L: Fab 3B6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0205
Polymers61,8923
Non-polymers1282
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-32 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.753, 71.867, 123.436
Angle α, β, γ (deg.)80.160, 85.050, 90.160
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain H
13chain D
23chain L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEARGARGchain AAA66 - 15924 - 117
21GLUGLUVALVALchain CCC69 - 16827 - 126
12GLNGLNLYSLYSchain BBB1 - 2201 - 220
22GLNGLNLYSLYSchain HHE1 - 2201 - 220
13GLNGLNTHRTHRchain DDD1 - 2121 - 212
23GLNGLNTHRTHRchain LLF1 - 2121 - 212

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 1 types, 2 molecules AC

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


Mass: 15289.139 Da / Num. of mol.: 2 / 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, 4 molecules BHDL

#2: Antibody Fab 3B6 heavy chain


Mass: 23916.699 Da / Num. of mol.: 2
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
#3: Antibody Fab 3B6 light chain


Mass: 22686.207 Da / Num. of mol.: 2
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 , 3 types, 390 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 3.72 Å3/Da / Density % sol: 66.93 % / Description: plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 40% MPD, 5% PEG 8000, 0.1M Na Cacodylate pH 6.5 / 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: 0.98 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.857→70.99 Å / Num. obs: 82724 / % possible obs: 89.6 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.059 / Net I/σ(I): 3.6
Reflection shellResolution: 1.858→2.044 Å / Redundancy: 3 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4136 / CC1/2: 0.635 / Rpim(I) all: 0.496 / Rrim(I) all: 0.701 / % possible all: 52.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VL5

2vl5


Resolution: 1.857→70.799 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 4035 4.88 %
Rwork0.2047 78601 -
obs0.2065 82636 55.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 233.76 Å2 / Biso mean: 55.7817 Å2 / Biso min: 16.25 Å2
Refinement stepCycle: final / Resolution: 1.857→70.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7841 0 30 386 8257
Biso mean--37.65 35.82 -
Num. residues----1058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118058
X-RAY DIFFRACTIONf_angle_d1.3110988
X-RAY DIFFRACTIONf_chiral_restr0.0481252
X-RAY DIFFRACTIONf_plane_restr0.0071406
X-RAY DIFFRACTIONf_dihedral_angle_d13.6482775
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A826X-RAY DIFFRACTION6.295TORSIONAL
12C826X-RAY DIFFRACTION6.295TORSIONAL
21B2466X-RAY DIFFRACTION6.295TORSIONAL
22H2466X-RAY DIFFRACTION6.295TORSIONAL
31D2389X-RAY DIFFRACTION6.295TORSIONAL
32L2389X-RAY DIFFRACTION6.295TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8572-1.87910.242730.24121042
1.8791-1.9020.222570.23531894
1.902-1.92610.3644220.2582846
1.9261-1.95140.2589230.24524259
1.9514-1.97820.2698330.263763613
1.9782-2.00640.2203460.24283217
2.0064-2.03640.281630.2231112423
2.0364-2.06820.2892830.2205169534
2.0682-2.10210.2304960.2162194539
2.1021-2.13840.25171140.2347196040
2.1384-2.17720.2589990.2222215643
2.1772-2.21910.23751170.2217211143
2.2191-2.26440.3297960.2379220945
2.2644-2.31370.26691120.2434234647
2.3137-2.36750.27171180.2548238449
2.3675-2.42670.25661570.2482257453
2.4267-2.49230.26291320.2612289758
2.4923-2.56570.28571480.2685307163
2.5657-2.64850.27861800.2561336868
2.6485-2.74310.29722100.2596368876
2.7431-2.8530.28582060.2572427987
2.853-2.98280.2942660.2376470296
2.9828-3.14010.27352290.2385483198
3.1401-3.33680.25922470.2035478697
3.3368-3.59440.22232530.1958478097
3.5944-3.95610.23162410.1813479497
3.9561-4.52850.18282340.1531472696
4.5285-5.70510.19922440.1618481197
5.7051-70.7990.22932560.19489499
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)
12.0598-0.0829-0.12412.44641.80611.3351-0.06140.4706-0.46390.26520.2067-0.11621.050.2566-0.05991.60020.05010.45371.1037-0.25740.773114.6096-63.9924-15.9069
20.5522-1.0558-1.56282.96593.92425.80730.2020.1577-0.1687-0.7664-0.1699-0.23770.14090.3682-0.59691.3354-0.02380.23091.6268-0.52560.71813.0887-63.102-22.7639
30.2425-0.0451-0.07941.8995-1.4782.895-0.18160.1510.1251-0.7799-0.131-0.81690.52680.6380.35120.9561-0.00390.26351.1895-0.03170.478719.9658-42.874-19.9124
42.68490.6669-1.81962.591-0.4832.2925-0.11320.7293-0.6029-0.59560.05610.29980.3431-0.170.02840.26350.0313-0.10790.4325-0.06380.3722-3.5277-54.05147.9787
51.977-0.85021.23122.9421-0.98571.98830.0223-0.11450.17390.1592-0.10140.1675-0.0483-0.12910.06930.14070.03610.01340.08570.07760.4987-27.7189-44.048723.7012
65.6176-0.9921-4.77795.36282.13724.3856-0.2023-0.0504-0.69440.06150.46780.1531.1248-0.5031-0.03331.553-0.2376-0.13011.24970.32971.2182-16.5285-26.713270.7598
71.3964-0.2329-0.63072.1012-2.00063.0046-0.1769-0.7577-0.92451.0038-0.0190.32620.8467-0.1616-0.43731.4764-0.14680.03441.25630.49730.7118-13.8372-23.389575.4229
85.84275.2397-5.61035.0093-5.17865.45740.278-1.0108-0.60171.60380.24411.67880.3132-1.3666-0.41931.0659-0.14890.26941.4760.11720.8109-21.3415-10.122969.5869
92.5390.0510.23832.41470.64890.1943-0.07260.8661-0.0646-0.7189-0.046-0.8966-0.64680.67390.21450.92830.05340.22061.33340.21141.0824-23.8897-11.940394.1256
101.5253-0.74520.61092.0578-0.06530.85340.22320.67070.5014-0.497-0.09680.1216-0.2765-0.29140.06150.28740.18420.01110.50280.26620.47642.8595-33.79973.8524
111.499-0.2211-0.28181.14540.99891.35790.1805-0.11110.2311-0.0348-0.2270.12130.284-0.0198-0.65230.20990.0542-0.03520.13210.14110.56-21.1187-33.865727.2596
121.9941-0.34930.15572.69920.62032.46930.0394-0.28380.14790.3329-0.19390.03330.1053-0.06780.06980.12490.0343-0.05320.13450.06970.586-21.4057-31.775534.5641
131.7073-0.5824-0.80491.92220.61731.0762-0.0027-0.6925-0.79680.6378-0.0006-0.27640.37550.0837-0.15740.3089-0.0437-0.20520.49420.30330.68781.6862-18.131946.6643
140.96660.24760.42391.69810.4980.9530.01660.0116-0.1979-0.1548-0.1267-0.0738-0.08330.07320.00360.1403-0.0507-0.030.04040.07630.69925.8606-8.094731.0963
153.3382-0.35390.87952.9564-0.06691.65150.1764-0.98080.0990.6551-0.0474-0.1631-0.28520.1701-0.09740.3185-0.1389-0.02960.4959-0.0240.2347-4.7881.933250.9277
162.20270.8233-1.18650.3077-0.44270.63780.493-0.30510.56770.2173-0.22610.2197-0.2219-0.009-0.22490.3155-0.10870.12040.2291-0.16070.50327.128513.09138.3327
172.4119-0.0738-0.44792.62330.02732.39130.07990.25590.0048-0.1758-0.15330.13290.18960.0253-0.01840.14390.0339-0.05110.09790.010.432919.52161.521622.3488
182.1028-0.5040.143.2-0.34313.06960.17190.58490.1425-0.576-0.185-0.28410.22360.24730.01730.18050.07320.02190.20070.04840.514423.01753.744316.8065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 66 through 90 )A66 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 125 )A91 - 125
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 159 )A126 - 159
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 125 )B1 - 125
5X-RAY DIFFRACTION5chain 'B' and (resid 126 through 220 )B126 - 220
6X-RAY DIFFRACTION6chain 'C' and (resid 69 through 90 )C69 - 90
7X-RAY DIFFRACTION7chain 'C' and (resid 91 through 133 )C91 - 133
8X-RAY DIFFRACTION8chain 'C' and (resid 134 through 146 )C134 - 146
9X-RAY DIFFRACTION9chain 'C' and (resid 147 through 168 )C147 - 168
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 103 )D1 - 103
11X-RAY DIFFRACTION11chain 'D' and (resid 104 through 132 )D104 - 132
12X-RAY DIFFRACTION12chain 'D' and (resid 133 through 212 )D133 - 212
13X-RAY DIFFRACTION13chain 'H' and (resid 1 through 125 )H1 - 125
14X-RAY DIFFRACTION14chain 'H' and (resid 126 through 220 )H126 - 220
15X-RAY DIFFRACTION15chain 'L' and (resid 1 through 103 )L1 - 103
16X-RAY DIFFRACTION16chain 'L' and (resid 104 through 116 )L104 - 116
17X-RAY DIFFRACTION17chain 'L' and (resid 117 through 174 )L117 - 174
18X-RAY DIFFRACTION18chain 'L' and (resid 175 through 212 )L175 - 212

+
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