[English] 日本語
Yorodumi
- PDB-4i1p: Human MALT1 (caspase-IG3) in complex with activity based-probe -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i1p
TitleHuman MALT1 (caspase-IG3) in complex with activity based-probe
Components
  • Mucosa-associated lymphoid tissue lymphoma translocation protein 1
  • tetrapeptide
KeywordsHYDROLASE / protease
Function / homology
Function and homology information


polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / regulation of T cell receptor signaling pathway / CBM complex / response to fungus / activation of NF-kappaB-inducing kinase activity / CLEC7A/inflammasome pathway / nuclear export / B cell activation ...polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / regulation of T cell receptor signaling pathway / CBM complex / response to fungus / activation of NF-kappaB-inducing kinase activity / CLEC7A/inflammasome pathway / nuclear export / B cell activation / small molecule binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / T cell proliferation / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-2 production / proteolysis involved in protein catabolic process / positive regulation of protein ubiquitination / positive regulation of interleukin-1 beta production / Activation of NF-kappaB in B cells / defense response / fibrillar center / CLEC7A (Dectin-1) signaling / positive regulation of T cell cytokine production / FCERI mediated NF-kB activation / ubiquitin-protein transferase activity / : / Downstream TCR signaling / positive regulation of NF-kappaB transcription factor activity / peptidase activity / T cell receptor signaling pathway / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / endopeptidase activity / protease binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / innate immune response / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein-containing complex / proteolysis / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Immunoglobulin-like - #3360 / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / MALT1 Ig-like domain / Rossmann fold - #1460 / Immunoglobulin domain / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : ...Immunoglobulin-like - #3360 / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / MALT1 Ig-like domain / Rossmann fold - #1460 / Immunoglobulin domain / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Immunoglobulin domain / Death-like domain superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsSchlauderer, F. / Lammens, K. / Hopfner, K.P.
CitationJournal: Chem.Biol. / Year: 2015
Title: Activity-Based Probes for Detection of Active MALT1 Paracaspase in Immune Cells and Lymphomas.
Authors: Eitelhuber, A.C. / Vosyka, O. / Nagel, D. / Bognar, M. / Lenze, D. / Lammens, K. / Schlauderer, F. / Hlahla, D. / Hopfner, K.P. / Lenz, G. / Hummel, M. / Verhelst, S.H. / Krappmann, D.
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
B: tetrapeptide
C: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
D: tetrapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,47014
Polymers89,8794
Non-polymers59010
Water2,090116
1
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
B: tetrapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2357
Polymers44,9402
Non-polymers2955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-5 kcal/mol
Surface area17560 Å2
MethodPISA
2
C: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
D: tetrapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2357
Polymers44,9402
Non-polymers2955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-6 kcal/mol
Surface area17780 Å2
MethodPISA
3
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
B: tetrapeptide
hetero molecules

C: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
D: tetrapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,47014
Polymers89,8794
Non-polymers59010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area6830 Å2
ΔGint-24 kcal/mol
Surface area32500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.243, 53.482, 78.740
Angle α, β, γ (deg.)90.00, 103.80, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT lymphoma-associated translocation / Paracaspase


Mass: 44189.820 Da / Num. of mol.: 2 / Fragment: UNP residues 339-719
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MALT1, MLT / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UDY8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein/peptide tetrapeptide /


Mass: 749.902 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic production of tetrapeptide
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Compound details4AR IS AMINO({(4S)-4-AMINO-6-[(2,6-DIMETHYLBENZOYL)OXY]-5-OXOHEXYL}AMINO)METHANIMINIUM. IN THIS ...4AR IS AMINO({(4S)-4-AMINO-6-[(2,6-DIMETHYLBENZOYL)OXY]-5-OXOHEXYL}AMINO)METHANIMINIUM. IN THIS STRUCTURE, 2,6-DIMETHYLBENZOIC ACID GROUP LEFT 4AR AND PEPTIDE IS BOUND COVALENTLY TO PROTEIN VIA C7 ATOM OF 4AR TO SG ATOM OF THE CYS 464 OF THE PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25 mM Mes, 75 mM calcium acetate, 10 % benzamidine hypochloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→44 Å / Num. obs: 27391 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.55 Å / % possible all: 69.2

-
Processing

Software
NameVersionClassification
DENZOdata reduction
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.403→43.939 Å / SU ML: 0.31 / σ(F): 1.99 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 1368 5 %
Rwork0.1984 --
obs0.2007 27345 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.403→43.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6100 0 40 116 6256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016236
X-RAY DIFFRACTIONf_angle_d1.3078414
X-RAY DIFFRACTIONf_dihedral_angle_d17.1082350
X-RAY DIFFRACTIONf_chiral_restr0.079959
X-RAY DIFFRACTIONf_plane_restr0.0081081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.403-2.48870.39031060.29612003X-RAY DIFFRACTION75
2.4887-2.58830.321270.29212405X-RAY DIFFRACTION90
2.5883-2.70610.35761400.26462670X-RAY DIFFRACTION99
2.7061-2.84870.30271390.25272677X-RAY DIFFRACTION100
2.8487-3.02720.33321420.24972679X-RAY DIFFRACTION99
3.0272-3.26080.29211410.23272676X-RAY DIFFRACTION100
3.2608-3.58880.24741430.20052703X-RAY DIFFRACTION100
3.5888-4.10780.23171410.17722689X-RAY DIFFRACTION100
4.1078-5.17410.19911420.16182700X-RAY DIFFRACTION99
5.1741-43.94650.20461470.17822775X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 17.9092 Å / Origin y: 7.8451 Å / Origin z: 18.4691 Å
111213212223313233
T0.4857 Å20.0092 Å2-0.1254 Å2-0.4336 Å2-0.0602 Å2--0.4983 Å2
L0.3771 °20.0052 °2-0.1333 °2-0.3731 °2-0.4012 °2--0.7997 °2
S-0.0174 Å °0.0741 Å °0.0058 Å °-0.1049 Å °0.0657 Å °0.129 Å °0.0579 Å °-0.15 Å °-0.0587 Å °
Refinement TLS groupSelection details: all

+
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