[English] 日本語
Yorodumi
- PDB-5vpl: CRYSTAL STRUCTURE OF DER F 1 COMPLEXED WITH FAB 4C1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vpl
TitleCRYSTAL STRUCTURE OF DER F 1 COMPLEXED WITH FAB 4C1
Components
  • 4C1 - HEAVY CHAIN
  • 4C1 - LIGHT CHAIN
  • Der f 1 variant
KeywordsHYDROLASE/IMMUNE SYSTEM / COMPLEX BETWEEN AN ALLERGEN AND FAB FRAGMENT OF 4C1 ANTIBODY / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


peptidase 1 (mite) / cysteine-type peptidase activity / immune response / proteolysis / extracellular space / extracellular region
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Der f 1 variant / Peptidase 1 / Anti-colorectal carcinoma light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Dermatophagoides farinae (American house dust mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChruszcz, M. / Vailes, L.D. / Chapman, M.D. / Pomes, A. / Minor, W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Molecular Determinants For Antibody Binding On Group 1 House Dust Mite Allergens.
Authors: Chruszcz, M. / Pomes, A. / Glesner, J. / Vailes, L.D. / Osinski, T. / Porebski, P.J. / Majorek, K.A. / Heymann, P.W. / Platts-Mills, T.A. / Minor, W. / Chapman, M.D.
History
DepositionMay 5, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMay 24, 2017ID: 3RVV
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.value / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Apr 13, 2022Group: Database references / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation_author / database_2
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms ..._audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 4, 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
A: Der f 1 variant
C: 4C1 - LIGHT CHAIN
D: 4C1 - HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2959
Polymers76,7863
Non-polymers5106
Water11,710650
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-16 kcal/mol
Surface area28340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.403, 79.428, 72.199
Angle α, β, γ (deg.)90.00, 105.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Antibody , 2 types, 2 molecules CD

#2: Antibody 4C1 - LIGHT CHAIN


Mass: 23937.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: Mus musculus (house mouse) / References: UniProt: Q7TS98
#3: Antibody 4C1 - HEAVY CHAIN


Mass: 27677.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: Mus musculus (house mouse)

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Der f 1 variant


Mass: 25170.975 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 99-321 / Source method: isolated from a natural source
Source: (natural) Dermatophagoides farinae (American house dust mite)
References: UniProt: I2CMD3, UniProt: P16311*PLUS
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 655 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1M HEPES, 18% W/V PEG12K, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2008 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 55979 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 23.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.557 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3D6S, 1MLB

3d6s
PDB Unreleased entry

1mlb


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19421 2783 5 %RANDOM
Rwork0.15169 ---
obs0.15376 53171 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0.05 Å2
2--1.02 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5093 0 31 650 5774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.025337
X-RAY DIFFRACTIONr_bond_other_d00.024676
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9427276
X-RAY DIFFRACTIONr_angle_other_deg3.798310900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4875664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96423.872235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31415840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8971530
X-RAY DIFFRACTIONr_chiral_restr0.1120.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0215959
X-RAY DIFFRACTIONr_gen_planes_other0.0260.021107
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1692.0052641
X-RAY DIFFRACTIONr_mcbond_other1.1682.0032640
X-RAY DIFFRACTIONr_mcangle_it1.8212.9973310
X-RAY DIFFRACTIONr_mcangle_other1.8222.9983311
X-RAY DIFFRACTIONr_scbond_it1.8682.262696
X-RAY DIFFRACTIONr_scbond_other1.8672.2582694
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.993.2983966
X-RAY DIFFRACTIONr_long_range_B_refined5.82424.856076
X-RAY DIFFRACTIONr_long_range_B_other5.71424.4836016
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 189 -
Rwork0.235 3809 -
obs--97.58 %
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)
10.8617-0.05280.09981.23060.36540.91450.0290.04150.0634-0.0331-0.03160.1297-0.0334-0.07960.00260.0109-0.0068-0.02170.0645-0.00790.128934.83812.83329.79
20.9068-0.27780.24010.5956-0.01791.06180.0185-0.1272-0.0748-0.02140.00920.04220.12340.0079-0.02760.0327-0.0046-0.00870.05890.00280.116643.0274.18134.436
31.1695-0.8463-0.32841.15860.16550.99880.0268-0.0408-0.015-0.0452-0.03640.03290.03650.07620.00960.02880.0072-0.01240.0631-0.01340.123976.762-0.64920.055
41.13090.3094-1.28592.1055-2.48275.54210.0372-0.15250.0146-0.0120.0408-0.1972-0.090.7043-0.07790.0042-0.03020.01320.2418-0.08740.1185100.9542.017-7.836
50.97040.244-0.65730.7125-0.27661.33030.03660.07190.0703-0.09360.01320.0128-0.1139-0.1447-0.04980.05060.0327-0.01180.0559-0.00260.118464.49312.427.996
61.3778-1.1921-0.65232.84391.27841.59960.08410.1210.0233-0.14390.0287-0.1245-0.0354-0.0012-0.11280.05370.0110.00380.0699-0.00690.065785.8980.656-13.403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 104
2X-RAY DIFFRACTION2A105 - 223
3X-RAY DIFFRACTION3C1 - 107
4X-RAY DIFFRACTION4C108 - 211
5X-RAY DIFFRACTION5D1 - 121
6X-RAY DIFFRACTION6D122 - 222

+
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://pdbjlvh1.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