[English] 日本語
Yorodumi
- PDB-6zl1: Crystal structure of human serum albumin in complex with the MCL-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zl1
TitleCrystal structure of human serum albumin in complex with the MCL-1 neutralizing Alphabody CMPX-383B
Components
  • Albumin
  • CMPX-383B
KeywordsDE NOVO PROTEIN / de novo protein design / 3 helical antiparallel coiled coil / cell penetrating Alphabody MCL-1 neutralizing Alphabody
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.272 Å
AuthorsPannecoucke, E. / Savvides, S.N. / Desmet, J. / Lasters, I.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: Sci Adv / Year: 2021
Title: Cell-penetrating Alphabody protein scaffolds for intracellular drug targeting.
Authors: Pannecoucke, E. / Van Trimpont, M. / Desmet, J. / Pieters, T. / Reunes, L. / Demoen, L. / Vuylsteke, M. / Loverix, S. / Vandenbroucke, K. / Alard, P. / Henderikx, P. / Deroo, S. / Baatz, F. ...Authors: Pannecoucke, E. / Van Trimpont, M. / Desmet, J. / Pieters, T. / Reunes, L. / Demoen, L. / Vuylsteke, M. / Loverix, S. / Vandenbroucke, K. / Alard, P. / Henderikx, P. / Deroo, S. / Baatz, F. / Lorent, E. / Thiolloy, S. / Somers, K. / McGrath, Y. / Van Vlierberghe, P. / Lasters, I. / Savvides, S.N.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Albumin
B: Albumin
C: CMPX-383B
D: CMPX-383B


Theoretical massNumber of molelcules
Total (without water)168,6434
Polymers168,6434
Non-polymers00
Water00
1
A: Albumin
C: CMPX-383B


Theoretical massNumber of molelcules
Total (without water)84,3222
Polymers84,3222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-12 kcal/mol
Surface area33290 Å2
MethodPISA
2
B: Albumin
D: CMPX-383B


Theoretical massNumber of molelcules
Total (without water)84,3222
Polymers84,3222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-13 kcal/mol
Surface area32900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.688, 231.346, 240.191
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Albumin


Mass: 69383.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Homo sapiens (human) / References: UniProt: P02768
#2: Protein CMPX-383B


Mass: 14938.014 Da / Num. of mol.: 2 / Mutation: I92T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.48 % / Description: Plate-like
Crystal growTemperature: 310.15 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 18% (w/v) PEG 3350, 0.1 M BIS-Tris pH 6.8, 0.2 M ammonium phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.272→115.673 Å / Num. obs: 24556 / % possible obs: 92.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 88.79 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.6
Reflection shellResolution: 3.272→3.389 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 0.52 / Num. unique obs: 1168 / CC1/2: 0.182 / CC star: 0.555 / % possible all: 44.11

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata scaling
PHASERphasing
Coot0.9 beta 2model building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MK8

3mk8


Resolution: 3.272→115.67 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.871 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.556
RfactorNum. reflection% reflectionSelection details
Rfree0.2809 1271 -RANDOM
Rwork0.2393 ---
obs0.2415 24556 91.8 %-
Displacement parametersBiso mean: 96.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.1284 Å20 Å20 Å2
2---1.9367 Å20 Å2
3----2.1918 Å2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refinement stepCycle: LAST / Resolution: 3.272→115.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8855 0 0 0 8855
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099006HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0212361HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2630SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1599HARMONIC5
X-RAY DIFFRACTIONt_it9006HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1398SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact7733SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion22.32
LS refinement shellResolution: 3.272→3.34 Å
RfactorNum. reflection% reflection
Rfree0.2883 20 -
Rwork0.2119 --
obs--32.04 %
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)
12.16590.83912.20460.67950.67631.88390.38790.24550.25920.2455-0.4162-0.80490.2592-0.80490.02830.0987-0.25780.19390.1211-0.1555-0.1454-6.2188-16.092323.8182
21.46380.2134-1.0690.9428-1.44021.62650.31410.0827-0.40810.0827-0.42580.8574-0.40810.85740.11160.1269-0.2796-0.11580.20090.0916-0.17967.181448.03329.2984
31.50481.56515.2886.12874.79948.08590.09660.06840.20760.06840.28710.2030.20760.203-0.38370.0198-0.17090.0449-0.142-0.05820.153724.25515.907840.9178
42.76140.7304-4.01430.9047-1.65327.75560.0148-0.14020.0869-0.14020.2349-0.09160.0869-0.0916-0.2497-0.1255-0.0862-0.0954-0.15480.01140.2436-22.216629.491849.1603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|29 - A|608 }A29 - 608
2X-RAY DIFFRACTION2{ B|29 - B|607 }B29 - 607
3X-RAY DIFFRACTION3{ C|3 - C|144 }C3 - 144
4X-RAY DIFFRACTION4{ D|2 - D|144 }D2 - 144

+
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