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- PDB-3o8e: Structure of extracelllar portion of CD46 in complex with Adenovi... -

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Basic information

Entry
Database: PDB / ID: 3o8e
TitleStructure of extracelllar portion of CD46 in complex with Adenovirus type 11 knob
Components
  • Fiber 36.1 kDa protein
  • Membrane cofactor proteinCD46
KeywordsCELL ADHESION/IMMUNE SYSTEM / short consensus repeat / complement control protein / fiber knob / virus-receptor interaction / cell adhesion-immunity complex / adenovirus / CD46 / CELL ADHESION - IMMUNE SYSTEM complex / CELL ADHESION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


sequestering of extracellular ligand from receptor / inner acrosomal membrane / negative regulation of complement activation, classical pathway / regulation of Notch signaling pathway / T cell mediated immunity / positive regulation of transforming growth factor beta production / positive regulation of memory T cell differentiation / positive regulation of regulatory T cell differentiation / adhesion receptor-mediated virion attachment to host cell / positive regulation of interleukin-10 production ...sequestering of extracellular ligand from receptor / inner acrosomal membrane / negative regulation of complement activation, classical pathway / regulation of Notch signaling pathway / T cell mediated immunity / positive regulation of transforming growth factor beta production / positive regulation of memory T cell differentiation / positive regulation of regulatory T cell differentiation / adhesion receptor-mediated virion attachment to host cell / positive regulation of interleukin-10 production / single fertilization / positive regulation of T cell proliferation / complement activation, classical pathway / Regulation of Complement cascade / viral capsid / virus receptor activity / signaling receptor activity / adaptive immune response / cell adhesion / symbiont entry into host cell / cadherin binding / negative regulation of gene expression / focal adhesion / innate immune response / host cell nucleus / positive regulation of gene expression / cell surface / extracellular space / extracellular exosome / nucleus / plasma membrane
Similarity search - Function
Membrane cofactor protein CD46 / Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain ...Membrane cofactor protein CD46 / Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Ribbon / Sandwich / Mainly Beta
Similarity search - Domain/homology
DITHIANE DIOL / Membrane cofactor protein / Fiber 36.1 kDa protein
Similarity search - Component
Biological speciesHuman adenovirus 11
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsPersson, B.D. / Schmitz, N.B. / Casasnovas, J.M. / Stehle, T.
CitationJournal: Plos Pathog. / Year: 2010
Title: Structure of the extracellular portion of CD46 provides insights into its interactions with complement proteins and pathogens.
Authors: Persson, B.D. / Schmitz, N.B. / Santiago, C. / Zocher, G. / Larvie, M. / Scheu, U. / Casasnovas, J.M. / Stehle, T.
History
DepositionAug 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Sep 7, 2011Group: Database references
Revision 1.4Oct 5, 2011Group: Database references
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software
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 / 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_ref_seq_dif / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fiber 36.1 kDa protein
B: Membrane cofactor protein
C: Fiber 36.1 kDa protein
D: Membrane cofactor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0109
Polymers104,4324
Non-polymers1,5785
Water6,810378
1
A: Fiber 36.1 kDa protein
B: Membrane cofactor protein
hetero molecules

A: Fiber 36.1 kDa protein
B: Membrane cofactor protein
hetero molecules

A: Fiber 36.1 kDa protein
B: Membrane cofactor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,65115
Polymers156,6486
Non-polymers3,0039
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
2
C: Fiber 36.1 kDa protein
D: Membrane cofactor protein
hetero molecules

C: Fiber 36.1 kDa protein
D: Membrane cofactor protein
hetero molecules

C: Fiber 36.1 kDa protein
D: Membrane cofactor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,37812
Polymers156,6486
Non-polymers1,7306
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)108.160, 108.160, 222.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsTHE BIOLOGICAL MOLECULE CAN BE DESCRIBED AS COMPOSED OF A THREEFOLD ARRANGEMENT OF THE TWO POLYMERIC CHAINS

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Components

#1: Protein Fiber 36.1 kDa protein


Mass: 23752.438 Da / Num. of mol.: 2 / Fragment: Adenovirus 11 knob (UNP RESIDUES 117-325)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 11 / Gene: CD46, MCP, MIC10 / Plasmid: pet-15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q772X2
#2: Protein Membrane cofactor protein / CD46 / Trophoblast leukocyte common antigen / TLX


Mass: 28463.486 Da / Num. of mol.: 2 / Fragment: CD46 SCR1-SCR4 (UNP RESIDUES 35-286)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell line (production host): CHINESE HAMSTER OVARY (CHO) CELLS
Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P15529
#3: 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.: 3
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
#4: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: microseeding, pH 8.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2009
RadiationMonochromator: yes / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→38.8 Å / Num. obs: 33537 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 51.82 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 8.4
Reflection shellResolution: 2.84→2.99 Å / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CKL and 3EXV

1ckl

3exv


Resolution: 2.84→38.8 Å / Cor.coef. Fo:Fc: 0.8844 / Cor.coef. Fo:Fc free: 0.872 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1682 5.02 %RANDOM
Rwork0.21 ---
obs0.21 33537 --
all-37568 --
Displacement parametersBiso mean: 50.01 Å2
Baniso -1Baniso -2Baniso -3
1--7.9998 Å20 Å20 Å2
2---7.9998 Å20 Å2
3---15.9995 Å2
Refine analyzeLuzzati coordinate error obs: 0.416 Å
Refinement stepCycle: LAST / Resolution: 2.84→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7053 0 100 378 7531
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0077369HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9110061HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2386SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes182HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1058HARMONIC5
X-RAY DIFFRACTIONt_it7369HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2
X-RAY DIFFRACTIONt_other_torsion18.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion10015
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact77734
LS refinement shellResolution: 2.84→2.94 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.3413 140 4.89 %
Rwork0.2591 2721 -
all0.2631 2861 -
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)
10.41030.3383-0.51560.35790.02870.13630.00170.01810.0058-0.0129-0.00940.0492-0.0108-0.03490.0077-0.09350.0168-0.0014-0.05750.0366-0.047136.2665-31.04922.2765
20.2228-0.13870.0686-0.16390.63880.00150.00470.0121-0.0125-0.0118-0.00450.02360.0096-0.0021-0.0002-0.04760.01820.017-0.01180.0293-0.004532.3465-25.550713.8915
30.2414-0.12670.73631.0505-0.16370.28430.0178-0.01070.02-0.00290.00050.0369-0.0216-0.0152-0.0183-0.1430.01970.0446-0.12580.0222-0.077941.0554-22.476219.3417
4-0.11710.06760.13510.1171-0.04350.15050.00070.0042-0.0013-0.0042-0.00160.00440.0014-0.00610.00090.0019-0.0046-0.0066-0.00610.0063-0.011436.1728-35.5076-1.5381
50.1169-0.02810.25650.12110.15910-0.0023-0.00550.00650.0109-0.0023-0.0008-0.00710.00030.0046-0.03960.00930.0036-0.02680.0039-0.030543.8822-28.604619.0047
60.8367-0.46170.6175-0.1460.45520.05340.0032-0.0123-0.00160.0085-0.00360.05360.0097-0.03480.0004-0.07750.00030.0075-0.04380.0187-0.042536.25931.1302-23.6099
70.4072-0.14110.1377-0.1750.51820.02040.0032-0.02120.010.01130.00080.0201-0.0023-0.0073-0.004-0.03180.001-0.0124-0.0086-0.0113-0.011632.343325.608-15.2521
80.20320.3022-0.07540.63040.0490.07840.01430.00440.0078-0.0118-0.00580.0051-0.0043-0.0173-0.0086-0.1035-0.01-0.0299-0.08260.0108-0.077741.685123.0457-23.2305
90.16640.05781.0440.37540.810.0318-0.002-0.02570.01130.02050.00820.0083-0.0092-0.01-0.0062-0.059-0.0059-0.0175-0.06410.0047-0.033939.609224.0408-12.5728
100.3309-0.11890.04860.0782-0.11470.07320.0028-0.0088-0.00150.0053-0.00320.0118-0.0032-0.01310.0004-0.0420.0021-0.0006-0.02560.0082-0.033441.940130.3586-17.6825
111.7888-0.42640.86122.4276-0.88340.90460.0011-0.01780.00280.0187-0.00610.0674-0.0171-0.05870.0050.00780.0380.04510.07740.03660.10520.7271-5.328921.8865
120.8070.17310.57051.3804-0.10290.73060.0035-0.0046-0.00950.0035-0.00120.03360.0087-0.0125-0.00230.0369-0.00330.00490.02530.03540.014541.0215-7.7149-8.4517
131.6960.4677-0.1762.76020.32231.4378-0.0080.00520.00140.00640.01110.01360.0111-0.003-0.00310.1167-0.00160.02240.0878-0.01320.025747.7659-5.8193-45.37
142.21121.1317-1.08212.52710.5282.8740.0035-0.00960.00210.0053-0.00050.01750.0026-0.0119-0.0030.1194-0.0116-0.00270.14710.02230.119927.58218.526-66.2485
151.20530.7168-0.85893.0245-0.54811.1019-0.00340.0240.0081-0.01880.00350.06350.0096-0.0605-0.00010.0468-0.0187-0.03510.05150.04930.10320.71455.3811-23.2574
160.4725-0.1439-0.26711.75720.4580.7511-0.00490.00770.015-0.00220.01170.0306-0.0096-0.02-0.00670.0435-0.00090.02230.01080.02930.003541.17928.04377.2476
172.1272-0.27020.57112.49890.06361.5405-0.0054-0.0101-0.0046-0.00350.01170.0153-0.01420.0014-0.00630.1262-0.0028-0.02620.092-0.00410.029247.33515.89544.5954
182.5555-0.84930.90172.19670.30163.00180.00020.00090.0026-0.00040.00160.0104-0.0027-0.0104-0.00170.11920.00740.01210.14740.01920.130326.821-9.445165.5006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|129 - 179}A129 - 179
2X-RAY DIFFRACTION2{A|180 - 208}A180 - 208
3X-RAY DIFFRACTION3{A|209 - 294}A209 - 294
4X-RAY DIFFRACTION4{A|295 - 306}A295 - 306
5X-RAY DIFFRACTION5{A|307 - 325}A307 - 325
6X-RAY DIFFRACTION6{C|129 - 179}C129 - 179
7X-RAY DIFFRACTION7{C|180 - 208}C180 - 208
8X-RAY DIFFRACTION8{C|209 - 265}C209 - 265
9X-RAY DIFFRACTION9{C|266 - 303}C266 - 303
10X-RAY DIFFRACTION10{C|304 - 325}C304 - 325
11X-RAY DIFFRACTION11{B|1 - 62}B1 - 62
12X-RAY DIFFRACTION12{B|63 - 126}B63 - 126
13X-RAY DIFFRACTION13{B|127 - 187}B127 - 187
14X-RAY DIFFRACTION14{B|188 - 252}B188 - 252
15X-RAY DIFFRACTION15{D|1 - 62}D1 - 62
16X-RAY DIFFRACTION16{D|63 - 125}D63 - 125
17X-RAY DIFFRACTION17{D|126 - 191}D126 - 191
18X-RAY DIFFRACTION18{D|192 - 252}D192 - 252

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