PDB-3l89: Human Adenovirus type 21 knob in complex with domains SCR1 and SC...

ID or keywords:

Entry

Database: PDB / ID: 3l89

Title

Human Adenovirus type 21 knob in complex with domains SCR1 and SCR2 of CD46 (membrane cofactor protein, MCP)

Components

Fiber protein
Membrane cofactor protein

Keywords

VIRAL PROTEIN/PROTEIN BINDING / Adenovirus / Fiber Knob / Viral Protein / Membrane cofactor protein / MCP / virus receptor complex / SCR / Short consensus repeat / CCP / complement control protein / Complement pathway / Glycoprotein / Host-virus interaction / Immune response / Innate immunity / Sushi2 / VIRAL PROTEIN-PROTEIN BINDING complex

Function / homology

Function and homology information

sequestering of extracellular ligand from receptor / inner acrosomal membrane / negative regulation of complement activation, classical pathway / positive regulation of transforming growth factor beta production / T cell mediated immunity / regulation of Notch signaling pathway / positive regulation of memory T cell differentiation / adhesion receptor-mediated virion attachment to host cell / positive regulation of regulatory T cell differentiation / positive regulation of interleukin-10 production ...
Similarity search - Function

Biological species

Human adenovirus 21

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.5 Å

Authors

Cupelli, K. / Stehle, T.

Citation

Journal: J.Virol. / Year: 2010
Title: Structure of adenovirus type 21 knob in complex with CD46 reveals key differences in receptor contacts among species B adenoviruses.
Authors: Cupelli, K. / Muller, S. / Persson, B.D. / Jost, M. / Arnberg, N. / Stehle, T.

History

Deposition	Dec 30, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 14, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jul 29, 2020	Group: 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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Sep 6, 2023	Group: 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 1.4	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3l89.cif.gz	700.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3l89.ent.gz	580.9 KB	Display	PDB format
PDBx/mmJSON format	3l89.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l8/3l89 ftp://data.pdbj.org/pub/pdb/validation_reports/l8/3l89	HTTPS FTP

-
Related structure data

Related structure data	3l88C 2o39S 1ckl S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5yua-1 22757 5k5s-d 9210 6mw7-2 22027 21428 22758 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3l88C

2o39S

1ckl

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#132 - Dec 2010 Adenovirus similarity (15) #231 - Mar 2019 Measles Virus Proteins similarity (7)

Deposited unit

A: Fiber protein

B: Fiber protein

C: Fiber protein

D: Fiber protein

E: Fiber protein

F: Fiber protein

G: Fiber protein

H: Fiber protein

I: Fiber protein

J: Fiber protein

K: Fiber protein

L: Fiber protein

M: Membrane cofactor protein

N: Membrane cofactor protein

O: Membrane cofactor protein

P: Membrane cofactor protein

Q: Membrane cofactor protein

R: Membrane cofactor protein

S: Membrane cofactor protein

T: Membrane cofactor protein

U: Membrane cofactor protein

V: Membrane cofactor protein

W: Membrane cofactor protein

X: Membrane cofactor protein

hetero molecules

442 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fiber protein

B: Fiber protein

C: Fiber protein

M: Membrane cofactor protein

N: Membrane cofactor protein

O: Membrane cofactor protein

hetero molecules

defined by author&software
110 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Fiber protein

E: Fiber protein

F: Fiber protein

P: Membrane cofactor protein

Q: Membrane cofactor protein

R: Membrane cofactor protein

hetero molecules

defined by author&software
110 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Fiber protein

H: Fiber protein

I: Fiber protein

S: Membrane cofactor protein

T: Membrane cofactor protein

U: Membrane cofactor protein

hetero molecules

defined by author&software
110 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: Fiber protein

K: Fiber protein

L: Fiber protein

V: Membrane cofactor protein

W: Membrane cofactor protein

X: Membrane cofactor protein

hetero molecules

defined by author&software
110 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.530, 107.710, 154.100
Angle α, β, γ (deg.)	90.01, 90.10, 104.70
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain A and (resseq 131:145 or resseq 153:220 or resseq...
2	1	1	chain B and (resseq 131:145 or resseq 153:220 or resseq...
3	1	1	chain C and (resseq 131:145 or resseq 153:220 or resseq...
1	1	2	chain D and (resseq 131:145 or resseq 153:220 or resseq...
2	1	2	chain E and (resseq 131:145 or resseq 153:220 or resseq...
3	1	2	chain F and (resseq 131:145 or resseq 153:220 or resseq...
1	1	3	chain G and (resseq 131:145 or resseq 153:220 or resseq...
2	1	3	chain H and (resseq 131:145 or resseq 153:220 or resseq...
3	1	3	chain I and (resseq 131:145 or resseq 153:220 or resseq...
1	1	4	chain J and (resseq 131:145 or resseq 153:220 or resseq...
2	1	4	chain K and (resseq 131:145 or resseq 153:220 or resseq...
3	1	4	chain L and (resseq 131:145 or resseq 153:220 or resseq...
1	1	5	chain M and (resseq 1:20 or resseq 26:40 or resseq 46:61 )
2	1	5	chain N and (resseq 1:20 or resseq 26:40 or resseq 46:61 )
3	1	5	chain O and (resseq 1:20 or resseq 26:40 or resseq 46:61 )
1	1	6	chain P and (resseq 1:20 or resseq 26:40 or resseq 46:62 )
2	1	6	chain Q and (resseq 1:20 or resseq 26:40 or resseq 46:62 )
3	1	6	chain R and (resseq 1:20 or resseq 26:40 or resseq 46:62 )
1	1	7	chain S and (resseq 1:20 or resseq 26:40 or resseq 46:61 )
2	1	7	chain T and (resseq 1:20 or resseq 26:40 or resseq 46:61 )
3	1	7	chain U and (resseq 1:20 or resseq 26:40 or resseq 46:61 )
1	1	8	chain V and (resseq 1:20 or resseq 26:40 or resseq 46:61 )
2	1	8	chain W and (resseq 1:20 or resseq 26:40 or resseq 46:61 )
3	1	8	chain X and (resseq 1:20 or resseq 26:40 or resseq 46:61 )
1	1	9	chain M and (resseq 64:78 or resseq 86:126 )
2	1	9	chain N and (resseq 64:78 or resseq 86:126 )
3	1	9	chain O and (resseq 64:78 or resseq 86:126 )
1	1	10	chain P and (resseq 64:78 or resseq 86:126 )
2	1	10	chain Q and (resseq 64:78 or resseq 86:126 )
3	1	10	chain R and (resseq 64:78 or resseq 86:126 )
1	1	11	chain S and (resseq 64:78 or resseq 86:126 )
2	1	11	chain T and (resseq 64:78 or resseq 86:126 )
3	1	11	chain U and (resseq 64:78 or resseq 86:126 )
1	1	12	chain V and (resseq 64:78 or resseq 86:126 )
2	1	12	chain W and (resseq 64:78 or resseq 86:126 )
3	1	12	chain X and (resseq 64:78 or resseq 86:126 )

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12

#1: Protein

Fiber protein

Mass: 22218.797 Da / Num. of mol.: 12 / Fragment: Ad21 fiber knob (UNP residues 123-323)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human adenovirus 21 / Strain: 2145 / Gene: 32608, L5 / Plasmid: pET15b / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q2KS96

#2: Protein

Membrane cofactor protein / Trophoblast leukocyte common antigen / TLX

Mass: 14517.551 Da / Num. of mol.: 12 / Fragment: CD46 SCR1 and SCR2 domains (UNP residues 35-160)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: 9606, CD46, MCP, MIC10 / Plasmid: PBJ5 / Production host:

Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-Lec3281 / References: UniProt: P15529

#3: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

Has protein modification

Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.44 Å³/Da / Density % sol: 64.27 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 6% PEG 8000, 0.1M LiCl, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2008
Radiation	Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9395 Å / Relative weight: 1
Reflection	Resolution: 3.5→48 Å / Num. obs: 71365 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 57.53 Å² / R_merge(I) obs: 0.179 / Net I/σ(I): 8.9
Reflection shell	Resolution: 3.5→3.62 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.355 / Mean I/σ(I) obs: 3.6 / % possible all: 74.9

-
Processing

Software

Name	Version	Classification
PHENIX	1.6_288	refinement
PDB_EXTRACT	3.005	data extraction
XDS		data scaling
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Ad21 fiber knob model, PDB ENTRY 2O39: CD46 SCR1-SCR2

2o39

Resolution: 3.5→47.991 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 2 / Phase error: 23.23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2389	3574	5.01 %
R_work	0.2037	-	-
obs	0.2055	71363	96.28 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 10.956 Å² / k_sol: 0.301 e/Å³

Displacement parameters

B_iso mean: 59.526 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	9.1802 Å²	-16.1912 Å²	-0.2235 Å²
2-	-	7.3689 Å²	-0.3624 Å²
3-	-	-	-16.5491 Å²

Refinement step

Cycle: LAST / Resolution: 3.5→47.991 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28961	0	56	0	29017

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	29807
X-RAY DIFFRACTION	f_angle_d	0.827	40613
X-RAY DIFFRACTION	f_dihedral_angle_d	15.781	10464
X-RAY DIFFRACTION	f_chiral_restr	0.055	4522
X-RAY DIFFRACTION	f_plane_restr	0.004	5237

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1282	X-RAY DIFFRACTION	POSITIONAL
1	2	B	1282	X-RAY DIFFRACTION	POSITIONAL	0.023
1	3	C	1282	X-RAY DIFFRACTION	POSITIONAL	0.022
2	1	D	1285	X-RAY DIFFRACTION	POSITIONAL
2	2	E	1285	X-RAY DIFFRACTION	POSITIONAL	0.022
2	3	F	1285	X-RAY DIFFRACTION	POSITIONAL	0.022
3	1	G	1288	X-RAY DIFFRACTION	POSITIONAL
3	2	H	1288	X-RAY DIFFRACTION	POSITIONAL	0.022
3	3	I	1291	X-RAY DIFFRACTION	POSITIONAL	0.021
4	1	J	1284	X-RAY DIFFRACTION	POSITIONAL
4	2	K	1284	X-RAY DIFFRACTION	POSITIONAL	0.023
4	3	L	1287	X-RAY DIFFRACTION	POSITIONAL	0.022
5	1	M	404	X-RAY DIFFRACTION	POSITIONAL
5	2	N	404	X-RAY DIFFRACTION	POSITIONAL	0.022
5	3	O	404	X-RAY DIFFRACTION	POSITIONAL	0.021
6	1	P	392	X-RAY DIFFRACTION	POSITIONAL
6	2	Q	392	X-RAY DIFFRACTION	POSITIONAL	0.018
6	3	R	404	X-RAY DIFFRACTION	POSITIONAL	0.02
7	1	S	379	X-RAY DIFFRACTION	POSITIONAL
7	2	T	379	X-RAY DIFFRACTION	POSITIONAL	0.016
7	3	U	383	X-RAY DIFFRACTION	POSITIONAL	0.018
8	1	V	405	X-RAY DIFFRACTION	POSITIONAL
8	2	W	405	X-RAY DIFFRACTION	POSITIONAL	0.025
8	3	X	409	X-RAY DIFFRACTION	POSITIONAL	0.02
9	1	M	425	X-RAY DIFFRACTION	POSITIONAL
9	2	N	425	X-RAY DIFFRACTION	POSITIONAL	0.025
9	3	O	433	X-RAY DIFFRACTION	POSITIONAL	0.023
10	1	P	430	X-RAY DIFFRACTION	POSITIONAL
10	2	Q	430	X-RAY DIFFRACTION	POSITIONAL	0.023
10	3	R	430	X-RAY DIFFRACTION	POSITIONAL	0.023
11	1	S	438	X-RAY DIFFRACTION	POSITIONAL
11	2	T	438	X-RAY DIFFRACTION	POSITIONAL	0.024
11	3	U	430	X-RAY DIFFRACTION	POSITIONAL	0.024
12	1	V	426	X-RAY DIFFRACTION	POSITIONAL
12	2	W	426	X-RAY DIFFRACTION	POSITIONAL	0.024
12	3	X	434	X-RAY DIFFRACTION	POSITIONAL	0.023

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.5-3.5461	0.3263	113	0.2676	2066	X-RAY DIFFRACTION	75
3.5461-3.5946	0.4104	105	0.2887	2002	X-RAY DIFFRACTION	75
3.5946-3.646	0.3025	109	0.2815	2044	X-RAY DIFFRACTION	75
3.646-3.7004	0.3188	136	0.2697	2597	X-RAY DIFFRACTION	98
3.7004-3.7582	0.2927	145	0.2508	2719	X-RAY DIFFRACTION	99
3.7582-3.8197	0.2777	143	0.2418	2659	X-RAY DIFFRACTION	100
3.8197-3.8856	0.2621	140	0.2428	2689	X-RAY DIFFRACTION	99
3.8856-3.9562	0.2568	138	0.2238	2701	X-RAY DIFFRACTION	99
3.9562-4.0323	0.236	144	0.2096	2663	X-RAY DIFFRACTION	99
4.0323-4.1145	0.2502	143	0.2054	2748	X-RAY DIFFRACTION	100
4.1145-4.2039	0.2112	137	0.1861	2648	X-RAY DIFFRACTION	99
4.2039-4.3017	0.2026	144	0.1839	2734	X-RAY DIFFRACTION	99
4.3017-4.4092	0.2139	139	0.1787	2638	X-RAY DIFFRACTION	99
4.4092-4.5283	0.2059	142	0.1769	2703	X-RAY DIFFRACTION	99
4.5283-4.6614	0.185	141	0.16	2654	X-RAY DIFFRACTION	99
4.6614-4.8118	0.2097	142	0.1694	2727	X-RAY DIFFRACTION	100
4.8118-4.9836	0.2102	144	0.1736	2678	X-RAY DIFFRACTION	99
4.9836-5.1829	0.2043	140	0.1677	2689	X-RAY DIFFRACTION	99
5.1829-5.4185	0.2083	142	0.1766	2654	X-RAY DIFFRACTION	99
5.4185-5.7037	0.2253	141	0.1732	2710	X-RAY DIFFRACTION	99
5.7037-6.0604	0.2127	140	0.1777	2665	X-RAY DIFFRACTION	99
6.0604-6.5273	0.2348	143	0.1854	2700	X-RAY DIFFRACTION	99
6.5273-7.1822	0.2202	142	0.175	2694	X-RAY DIFFRACTION	99
7.1822-8.217	0.1821	140	0.1621	2635	X-RAY DIFFRACTION	98
8.217-10.3355	0.192	141	0.171	2691	X-RAY DIFFRACTION	99
10.3355-47.9954	0.2205	140	0.2254	2681	X-RAY DIFFRACTION	99

-
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

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi