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- PDB-6ion: The complex of C4.4A with its antibody 11H10 Fab fragment -

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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 space / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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 )

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