[English] 日本語
Yorodumi
- PDB-1pew: High Resolution Crystal Structure of Jto2, a mutant of the non-am... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pew
TitleHigh Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto
ComponentsJto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
KeywordsIMMUNE SYSTEM / Beta Sheet
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / antigen binding / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin lambda variable 6-57 / Immunoglobulin lambda variable 6-57
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDealwis, C. / Gupta, V. / Wilkerson, M.
CitationJournal: J.Mol.Recog. / Year: 2004
Title: Structural basis of light chain amyloidogenicity: comparison of the thermodynamic properties, fibrillogenic potential and tertiary structural features of four V(lambda)6 proteins
Authors: Wall, J.S. / Gupta, V. / Wilkerson, M. / Schell, M. / Loris, R. / Adams, P. / Solomon, A. / Stevens, F. / Dealwis, C.
History
DepositionMay 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
B: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2486
Polymers23,7982
Non-polymers4504
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
B: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules

A: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
B: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,49512
Polymers47,5964
Non-polymers8998
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x,y,-z-11
Buried area5200 Å2
ΔGint-72 kcal/mol
Surface area19390 Å2
MethodPISA, PQS
3
B: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules

B: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules

A: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules

A: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,49512
Polymers47,5964
Non-polymers8998
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_524x,-y-3,-z-1/21
crystal symmetry operation2_525-x,-y-3,z+1/21
crystal symmetry operation5_554-x,y,-z-11
Buried area3780 Å2
ΔGint-59 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.577, 73.577, 92.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Cell settingtetragonal
Space group name H-MP4122

-
Components

#1: Antibody Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN / immunoglobulin lambda light chain VLJ region


Mass: 11898.972 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN / Mutation: D29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Jto / Plasmid: pET-27b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21DE3 / References: UniProt: P06317, UniProt: P01721*PLUS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Na Acetate, 0.8M Amm. Sulfate, 100mM Cadmium chloride, 10% n-Decyl-B-D-maltoside, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.5418 Å
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: Sep 15, 2001
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. all: 32368 / Num. obs: 31495 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Rsym value: 0.066 / Net I/σ(I): 20.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 3339 / Rsym value: 0.515 / % possible all: 93.8

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CD0

1cd0


Resolution: 1.6→8 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.907 / SU B: 3.385 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.125 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27291 1633 4.9 %RANDOM
Rwork0.2522 ---
all0.295 ---
obs0.2533 31495 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.751 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 4 104 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211687
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9392288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9625212
X-RAY DIFFRACTIONr_chiral_restr0.0820.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021318
X-RAY DIFFRACTIONr_nbd_refined0.2280.2777
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2340.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3520.211
X-RAY DIFFRACTIONr_mcbond_it0.531.51070
X-RAY DIFFRACTIONr_mcangle_it0.90421727
X-RAY DIFFRACTIONr_scbond_it1.5653617
X-RAY DIFFRACTIONr_scangle_it2.2344.5561
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 109
Rwork0.356 2114
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)
14.40540.0468-0.22153.30520.63533.7139-0.172-0.2481-0.25590.0664-0.04740.09790.11940.04040.21940.1128-0.00180.01690.00110.00850.078111.9083-100.4335-60.9006
28.3907-0.0137-4.75092.8506-0.92836.37370.81330.80940.77870.2501-0.09720.2009-0.951-0.8149-0.71610.24950.19530.11790.26270.15440.16868.0555-117.2196-37.5231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 108
2X-RAY DIFFRACTION2B1 - 108

+
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