[English] 日本語
Yorodumi
- PDB-6ion: The complex of C4.4A with its antibody 11H10 Fab fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ion
TitleThe complex of C4.4A with its antibody 11H10 Fab fragment
Components
  • Ly6/PLAUR domain-containing protein 3
  • anti-C4.4A antibody 11H10, heavy chain
  • anti-C4.4A antibody 11H10, light chain
KeywordsIMMUNE SYSTEM / uPAR / three-fingered fold / LU domain
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of smooth muscle cell apoptotic process / side of membrane / laminin binding / cell-matrix adhesion / : / extracellular region / plasma membrane
Similarity search - Function
u-PAR/Ly-6 domain / Ly-6 antigen / uPA receptor -like domain / Ly-6 antigen/uPA receptor-like / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ly6/PLAUR domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsHuang, M.D. / Jiang, Y.B. / Yuan, C. / Lin, L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670739 China
National Natural Science Foundation of China31570745 China
National Natural Science Foundation of China31370737 China
CitationJournal: Int J Biol Sci / Year: 2020
Title: Crystal Structures of Human C4.4A Reveal the Unique Association of Ly6/uPAR/alpha-neurotoxin Domain
Authors: Jiang, Y.B. / Lin, L. / Chen, S. / Jiang, L.G. / Kriegbaum, M.C. / Gardsvoll, H. / Hansen, L.V. / Li, J. / Ploug, M. / Yuan, C. / Huang, M.D.
History
DepositionOct 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_abbrev ..._chem_comp.type / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _citation.country / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: anti-C4.4A antibody 11H10, light chain
H: anti-C4.4A antibody 11H10, heavy chain
A: Ly6/PLAUR domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5566
Polymers68,6903
Non-polymers8673
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-18 kcal/mol
Surface area26520 Å2
Unit cell
Length a, b, c (Å)51.860, 63.960, 107.710
Angle α, β, γ (deg.)90.00, 96.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody anti-C4.4A antibody 11H10, light chain


Mass: 23684.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody anti-C4.4A antibody 11H10, heavy chain


Mass: 23860.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein Ly6/PLAUR domain-containing protein 3 / GPI-anchored metastasis-associated protein C4.4A homolog / Matrigel-induced gene C4 protein / MIG-C4


Mass: 21143.783 Da / Num. of mol.: 1 / Fragment: UNP residues 31-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C4.4A / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: O95274
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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
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: 52.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Tris-HCl pH 7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→40.144 Å / Num. obs: 18267 / % possible obs: 98.91 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.1134 / Net I/σ(I): 8.9
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.8406 / Num. unique obs: 1809

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CLE, 3BT2

3cle

3bt2


Resolution: 2.75→40.144 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.57
RfactorNum. reflection% reflection
Rfree0.2545 926 5.07 %
Rwork0.1967 --
obs0.1995 18266 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.75→40.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 56 0 4603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134725
X-RAY DIFFRACTIONf_angle_d1.8956459
X-RAY DIFFRACTIONf_dihedral_angle_d8.0952765
X-RAY DIFFRACTIONf_chiral_restr0.108742
X-RAY DIFFRACTIONf_plane_restr0.014826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.8950.34591400.29142464X-RAY DIFFRACTION99
2.895-3.07630.30311380.25072437X-RAY DIFFRACTION99
3.0763-3.31370.27531190.23792467X-RAY DIFFRACTION99
3.3137-3.6470.27271350.18712455X-RAY DIFFRACTION99
3.647-4.17420.24611260.18282490X-RAY DIFFRACTION99
4.1742-5.25720.20891290.15632498X-RAY DIFFRACTION99
5.2572-40.14860.2471390.19672529X-RAY DIFFRACTION99
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)
19.21420.0125-4.15562.27171.76443.4438-0.05870.74371.6604-1.11330.25060.0231-1.83230.3904-0.14540.8781-0.2303-0.14210.61710.22470.80698.39652.936224.7665
24.88071.48240.95237.9291.06995.6938-0.32850.27410.09-0.86540.04420.258-0.44850.71020.31450.3635-0.0790.03680.387-0.00660.527412.3628-4.732431.6642
37.08231.0918-0.22155.8983-1.29365.32060.28340.38710.8522-0.63710.17820.3658-0.31650.3925-0.56080.2981-0.05330.08550.36960.06220.46017.2754-5.524831.1819
41.6598-1.3046-0.48684.63380.05652.0894-0.32590.81090.7650.08910.7548-0.2636-0.5896-0.29511.17180.8599-0.30660.03380.8730.53930.75264.51573.05219.9204
51.9881.08321.5699.03933.02913.3175-0.7099-0.71960.2072-2.1219-0.79951.3831-0.2004-0.15221.22721.0816-0.074-0.28981.8860.1420.851-22.4247-4.8794-0.5987
65.91890.2061-1.36031.96770.21712.19290.48570.66190.79950.204-0.15120.4251-0.865-0.4526-0.29410.9893-0.01520.00491.03170.3090.775-11.94834.29816.0568
72.077-0.876-3.25135.4087-2.02647.3942-0.4676-0.82360.47410.4740.70090.2426-1.8251-0.789-0.62431.26020.0935-0.06941.0785-0.01250.916-20.48636.37459.9468
89.14343.08726.52152.00852.50398.4599-0.31551.3221-0.1314-0.70340.0963-1.48530.2192.73810.12250.62830.0683-0.02541.03290.07820.77571.0743-3.4858.3995
93.52912.20654.10993.58772.46825.23010.3788-0.72972.6119-0.3089-0.45570.89320.1053-1.02590.2360.64620.15080.01691.13440.05451.0726-24.85733.64223.1372
101.06981.0081.83195.04011.84457.5148-0.4331.33021.9243-0.34760.33090.3515-1.4868-0.05980.15881.03810.10890.15621.20480.38411.1509-13.69729.6385-1.1773
111.39442.31550.00185.8305-1.39846.26540.38760.5146-1.0048-0.5605-0.11510.5690.2187-0.8904-0.28870.3803-0.0032-0.03440.5112-0.03480.7722-12.0183-20.737931.3214
124.63292.42684.7144.24761.24417.99240.22060.62570.1311-0.247-0.3373-0.30130.85390.339-0.0110.38280.03840.08430.3399-0.05030.64690.9115-24.682640.0143
134.32491.1892.19070.576-0.58647.5814-0.0763-0.32960.44170.1094-0.130.2484-0.4601-0.52790.09160.28030.03990.05870.3047-0.07290.6546-4.4705-14.445841.9207
145.2372.92930.86482.10820.11175.38030.14860.1876-0.7118-0.1350.12470.4639-0.0837-0.4397-0.18750.2760.05620.05270.407-0.0050.6409-3.3056-17.836735.6469
152.3626-0.37481.97673.08950.5441.97030.2741.1046-0.137-0.44250.226-0.54270.0943-1.192-0.71150.4289-0.00660.08641.35390.1280.726-19.4158-12.07818.2999
168.38453.63985.25077.2207-1.93357.1228-0.30620.9152-0.6245-0.48741.0301-0.31670.563-0.0898-0.50090.71450.0713-0.07640.7948-0.11750.6196-9.3304-13.95546.3044
172.17651.21471.2158.0978-3.14862.59751.01980.24750.57590.27871.06370.2184-0.9619-0.0413-2.06090.6370.1380.05111.3049-0.01040.5072-16.3847-8.347110.2882
187.6827-1.93771.78935.3955-2.74861.49771.03160.8614-0.6534-2.3442-0.4664-0.69681.55150.04990.32411.6487-0.08950.45122.0083-0.4520.702-9.4821-11.461-12.159
191.7960.4587-2.91550.3269-1.30446.14020.37880.9118-0.8429-0.48010.8636-0.2580.99380.1725-0.57721.3677-0.21690.07641.235-0.43710.8341-16.7838-19.32653.0629
201.7124-1.2987-2.6087.81110.63094.2555-0.5347-1.7215-2.94380.5793-0.031.16310.1296-0.35090.51030.4483-0.02110.09740.78680.11220.9175-7.2729-20.710673.0598
211.48462.3814-1.30413.9329-1.75055.42130.1441-1.0727-0.02740.9705-0.65991.0988-0.9060.0158-0.1305-0.0901-0.22860.26610.6408-0.2040.9095-7.1013-11.925767.1155
224.704-1.1839-3.4270.58141.08522.59640.0928-0.0269-0.2893-0.23720.01570.4618-0.2052-0.2864-0.070.2322-0.02520.03080.4440.03110.9280.2168-12.577560.688
234.18611.1109-1.84891.243-0.89392.81250.10470.22960.39760.27160.27910.16990.0204-0.2339-0.32680.36070.0992-0.04430.3363-0.04960.7929-2.8794-16.360660.2233
246.2486-0.30613.4892.5571-3.066.37780.072-0.36970.1412-0.0139-0.216-0.1018-0.22280.03170.18390.27580.0340.07140.3042-0.01980.613419.1774-20.168760.0489
258.62330.4582-2.65272.2186-0.51865.74630.143-0.85270.27620.3811-0.14010.0132-0.1438-0.0361-0.08510.2342-0.00420.07820.3989-0.05460.70810.1023-12.464166.0255
264.922-1.4079-3.20812.8504-0.81216.7083-0.1326-0.05660.45250.5945-0.2956-1.438-1.0570.2976-0.25270.4130.0358-0.01030.34020.05871.195515.4567-5.923957.8888
271.2307-2.26380.74494.5813-0.33955.7106-0.1915-0.06520.33540.3608-0.2233-1.1672-0.64540.74250.16840.3087-0.0358-0.01430.45830.13550.79521.6375-9.609163.2544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 2 through 18 )
2X-RAY DIFFRACTION2chain 'L' and (resid 19 through 75 )
3X-RAY DIFFRACTION3chain 'L' and (resid 76 through 103 )
4X-RAY DIFFRACTION4chain 'L' and (resid 104 through 114 )
5X-RAY DIFFRACTION5chain 'L' and (resid 115 through 129 )
6X-RAY DIFFRACTION6chain 'L' and (resid 130 through 151 )
7X-RAY DIFFRACTION7chain 'L' and (resid 152 through 164 )
8X-RAY DIFFRACTION8chain 'L' and (resid 165 through 175 )
9X-RAY DIFFRACTION9chain 'L' and (resid 176 through 198 )
10X-RAY DIFFRACTION10chain 'L' and (resid 199 through 214 )
11X-RAY DIFFRACTION11chain 'H' and (resid 2 through 17 )
12X-RAY DIFFRACTION12chain 'H' and (resid 18 through 33 )
13X-RAY DIFFRACTION13chain 'H' and (resid 34 through 74 )
14X-RAY DIFFRACTION14chain 'H' and (resid 75 through 114 )
15X-RAY DIFFRACTION15chain 'H' and (resid 115 through 150 )
16X-RAY DIFFRACTION16chain 'H' and (resid 151 through 173 )
17X-RAY DIFFRACTION17chain 'H' and (resid 174 through 188 )
18X-RAY DIFFRACTION18chain 'H' and (resid 189 through 198 )
19X-RAY DIFFRACTION19chain 'H' and (resid 199 through 217 )
20X-RAY DIFFRACTION20chain 'A' and (resid 1 through 23 )
21X-RAY DIFFRACTION21chain 'A' and (resid 24 through 40 )
22X-RAY DIFFRACTION22chain 'A' and (resid 41 through 68 )
23X-RAY DIFFRACTION23chain 'A' and (resid 69 through 108 )
24X-RAY DIFFRACTION24chain 'A' and (resid 109 through 140 )
25X-RAY DIFFRACTION25chain 'A' and (resid 141 through 164 )
26X-RAY DIFFRACTION26chain 'A' and (resid 165 through 178 )
27X-RAY DIFFRACTION27chain 'A' and (resid 179 through 200 )

+
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