[English] 日本語
Yorodumi
- PDB-5vco: THE CRYSTAL STRUCTURE OF DER P 1 ALLERGEN COMPLEXED WITH FAB FRAG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vco
TitleTHE CRYSTAL STRUCTURE OF DER P 1 ALLERGEN COMPLEXED WITH FAB FRAGMENT OF MAB 10B9
Components
  • HEAVY CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
  • LIGHT CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
  • PEPTIDASE 1
KeywordsIMMUNE SYSTEM / ALLERGEN / ANTIBODY
Function / homology
Function and homology information


peptidase 1 (mite) / cysteine-type peptidase activity / proteolysis / extracellular region / metal ion binding
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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Peptidase 1 / Der p 1 allergen
Similarity search - Component
Biological speciesMus musculus (house mouse)
Dermatophagoides pteronyssinus (European house dust mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsOsinski, T. / Majorek, K.A. / Pomes, A. / Offermann, L.R. / Osinski, S. / Glesner, J. / Vailes, L.D. / Chapman, M.D. / Minor, W. / Chruszcz, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI077653 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM53163 United States
CitationJournal: J. Immunol. / Year: 2015
Title: Structural Analysis of Der p 1-Antibody Complexes and Comparison with Complexes of Proteins or Peptides with Monoclonal Antibodies.
Authors: Osinski, T. / Pomes, A. / Majorek, K.A. / Glesner, J. / Offermann, L.R. / Vailes, L.D. / Chapman, M.D. / Minor, W. / Chruszcz, M.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionApr 26, 2017ID: 4PP2
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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 1.4Apr 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 1.5Apr 27, 2022Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.6Oct 4, 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
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LIGHT CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
B: HEAVY CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
C: LIGHT CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
D: HEAVY CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
E: PEPTIDASE 1
F: PEPTIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,38310
Polymers144,8616
Non-polymers5234
Water39622
1
A: LIGHT CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
B: HEAVY CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
F: PEPTIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6925
Polymers72,4303
Non-polymers2612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: LIGHT CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
D: HEAVY CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
E: PEPTIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6925
Polymers72,4303
Non-polymers2612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.685, 74.852, 184.103
Angle α, β, γ (deg.)90.00, 97.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPARGARGAA1 - 2111 - 211
21ASPASPARGARGCC1 - 2111 - 211
12GLUGLUARGARGBB1 - 2221 - 222
22GLUGLUARGARGDD1 - 2221 - 222
13THRTHRLEULEUEE1 - 2221 - 222
23THRTHRLEULEUFF1 - 2221 - 222

NCS ensembles :
ID
2
1
3

-
Components

-
Antibody , 2 types, 4 molecules ACBD

#1: Antibody LIGHT CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY


Mass: 23280.555 Da / Num. of mol.: 2
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)
#2: Antibody HEAVY CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY


Mass: 24135.102 Da / Num. of mol.: 2
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, 4 molecules EF

#3: Protein PEPTIDASE 1 / ALLERGEN DER P I / MAJOR MITE FECAL ALLERGEN DER P 1


Mass: 25014.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Dermatophagoides pteronyssinus (European house dust mite)
References: UniProt: Q3HWZ5, UniProt: P08176*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.: 2
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 , 2 types, 24 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 MM NA ACETATE, 8% W/V PEG 4000, 15% MPD, PH 4.5
PH range: 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.51201 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2011 / Details: BERYLLIUM LENSES
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.51201 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 36141 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 55.2 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 14.5
Reflection shellResolution: 2.74→2.79 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.684 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMAC5.7.0029refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F5V, 3RVT

3f5v

3rvt


Resolution: 2.74→47.26 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.89 / SU B: 33.171 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.393 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1786 5 %RANDOM
Rwork0.2 ---
obs0.203 34176 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.94 Å2
Baniso -1Baniso -2Baniso -3
1-7.5 Å2-0 Å2-4.07 Å2
2---5.09 Å2-0 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 2.74→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9866 0 30 22 9918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0210151
X-RAY DIFFRACTIONr_bond_other_d0.0010.028992
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.93813892
X-RAY DIFFRACTIONr_angle_other_deg0.7153.00320579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23951292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46324.07430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.713151455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9181546
X-RAY DIFFRACTIONr_chiral_restr0.0670.21566
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022392
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A11990.09
12C11990.09
21B11680.06
22D11680.06
31E13120.09
32F13120.09
LS refinement shellResolution: 2.74→2.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 118 -
Rwork0.32 2482 -
obs--97.6 %
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)
10.6547-0.08530.0720.78110.4121.0472-0.0144-0.03120.0282-0.07390.0252-0.0237-0.00270.0256-0.01080.10510.01040.00220.1430.02110.12715.643-19.421109.338
21.50020.4143-0.74970.4195-0.05790.74710.03970.02530.10670.0383-0.0050.04330.00330.024-0.03460.0470.0116-0.00020.1476-0.01720.1821-16.193-14.959138.871
30.63770.3997-0.16140.7193-0.37221.0303-0.024-0.0174-0.02160.0004-0.0182-0.00920.0239-0.03920.04230.12540.0065-0.04150.1182-0.00530.1275-14.683-22.83497.863
41.95460.7754-0.62230.5028-0.35480.42490.0236-0.00250.0015-0.02620.04470.0258-0.0384-0.0508-0.06830.1198-0.0009-0.01760.14630.00860.1274-9.665-21.579101.231
50.5306-0.19990.35751.18130.97321.4152-0.0310.00390.0894-0.03460.0118-0.0347-0.0587-0.0840.01930.04540.0113-0.00730.17170.04810.1993-24.157-10.277125.309
60.27010.1993-0.15790.7665-0.63951.4362-0.0048-0.02610.0481-0.0082-0.01280.05230.0385-0.00370.01760.00910.0130.03540.2055-0.02290.19375.0771.76818.976
71.46320.31511.02960.41520.31241.1732-0.0284-0.01530.01790.06960.0030.0123-0.0476-0.05050.02530.0384-0.00590.0390.16750.02130.153221.08-1.48451.783
80.30160.26130.47651.07630.68681.1887-0.01520.0689-0.00840.00960.0014-0.0337-0.04840.07530.01370.01820.00520.04970.20350.01880.209527.1674.84210.75
91.11030.49980.80640.87470.35350.7039-0.0090.0383-0.0189-0.04390.0346-0.0766-0.0402-0.005-0.02560.02080.0110.04770.21670.0120.196321.7063.65713.421
100.60730.3884-0.00391.2259-0.17720.51580.0277-0.0056-0.02040.0263-0.03540.03180.01410.00610.00770.01430.00220.04680.20640.00140.1831.184-7.61340.645
110.4924-0.25060.06550.4809-0.09240.34460.01210.02170.0152-0.0303-0.01030.01010.04820.0073-0.00180.0211-0.00510.04480.1896-0.0090.16980.5976.208-15.218
120.4356-0.0069-0.1030.4810.14240.1046-0.01260.0201-0.0704-0.0428-0.01420.0283-0.07550.0190.02670.1829-0.0137-0.03050.11870.00810.094515.039-23.7476.139
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2A106 - 211
3X-RAY DIFFRACTION3B1 - 80
4X-RAY DIFFRACTION4B81 - 120
5X-RAY DIFFRACTION5B121 - 222
6X-RAY DIFFRACTION6C1 - 105
7X-RAY DIFFRACTION7C106 - 211
8X-RAY DIFFRACTION8D1 - 80
9X-RAY DIFFRACTION9D81 - 120
10X-RAY DIFFRACTION10D121 - 222
11X-RAY DIFFRACTION11E1 - 222
12X-RAY DIFFRACTION12F1 - 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://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