PDB-7zxk: Human IL-27 in complex with neutralizing SRF388 FAb fragment

ID or keywords:

Entry

Database: PDB / ID: 7zxk

Title

Human IL-27 in complex with neutralizing SRF388 FAb fragment

Components

(Interleukin-27 subunit ...) x 2
SRF388 Heavy Chain
SRF388 Light Chain

Keywords

CYTOKINE / heterodimer / neutralizing / antibody

Function / homology

Function and homology information

interleukin-27 receptor binding / regulation of T-helper 1 cell differentiation / response to Gram-positive bacterium / positive regulation of alpha-beta T cell proliferation / Interleukin-27 signaling / Interleukin-35 Signalling / cytokine receptor activity / T-helper 1 type immune response / regulation of T cell proliferation / humoral immune response ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Bloch, Y. / Skladanowska, K. / Strand, J. / Welin, M. / Logan, D. / Hill, J. / Savvides, S.N.

Funding support

Belgium, 1items

Citation

Journal: Cell Rep / Year: 2022
Title: Structural basis of activation and antagonism of receptor signaling mediated by interleukin-27.
Authors: Skladanowska, K. / Bloch, Y. / Strand, J. / White, K.F. / Hua, J. / Aldridge, D. / Welin, M. / Logan, D.T. / Soete, A. / Merceron, R. / Murphy, C. / Provost, M. / Bazan, J.F. / Hunter, C.A. ...

History

Deposition	May 21, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7zxk.cif.gz	723.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7zxk.ent.gz	530.2 KB	Display	PDB format
PDBx/mmJSON format	7zxk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7zxk_validation.pdf.gz	505.6 KB	Display	wwPDB validaton report
Full document	7zxk_full_validation.pdf.gz	520.2 KB	Display
Data in XML	7zxk_validation.xml.gz	58.9 KB	Display
Data in CIF	7zxk_validation.cif.gz	83.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zx/7zxk ftp://data.pdbj.org/pub/pdb/validation_reports/zx/7zxk	HTTPS FTP

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Related structure data

Related structure data	7zg0C 5fucS 5ijkS 6azmS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #128 - Aug 2010 Interferons similarity (1) #52 - Apr 2004 Growth Hormone similarity (2) #122 - Feb 2010 Enhanceosome similarity (2) #185 - May 2015 Titin similarity (1) #149 - May 2012 Leptin similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Interleukin-27 subunit alpha

B: Interleukin-27 subunit beta

C: Interleukin-27 subunit alpha

D: Interleukin-27 subunit beta

H: SRF388 Heavy Chain

I: SRF388 Light Chain

J: SRF388 Heavy Chain

L: SRF388 Light Chain

hetero molecules

193 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Interleukin-27 subunit alpha

B: Interleukin-27 subunit beta

I: SRF388 Light Chain

J: SRF388 Heavy Chain

hetero molecules

defined by author
Evidence: homology, pdb 7zg0
96.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Interleukin-27 subunit alpha

D: Interleukin-27 subunit beta

H: SRF388 Heavy Chain

L: SRF388 Light Chain

hetero molecules

defined by author
96.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.806, 104.622, 121.754
Angle α, β, γ (deg.)	90.000, 98.650, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Interleukin-27 subunit ... , 2 types, 4 molecules ACBD

#1: Protein	Interleukin-27 subunit alpha / IL-27 subunit alpha / IL-27-A / IL27-A / Interleukin-30 / p28 Mass: 24562.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Peprotech cat number 200-38 / Source: (gene. exp.) Homo sapiens (human) / Gene: IL27, IL27A, IL30 / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8NEV9
#2: Protein	Interleukin-27 subunit beta / IL-27 subunit beta / IL-27B / Epstein-Barr virus-induced gene 3 protein / EBV-induced gene 3 protein Mass: 23338.732 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Peprotech cat number 200-38 / Source: (gene. exp.) Homo sapiens (human) / Gene: EBI3, IL27B / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q14213

#1: Protein

Interleukin-27 subunit alpha / IL-27 subunit alpha / IL-27-A / IL27-A / Interleukin-30 / p28

Mass: 24562.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Peprotech cat number 200-38 / Source: (gene. exp.)

Homo sapiens (human) / Gene: IL27, IL27A, IL30 / Cell (production host): HEK293 / Production host:

Homo sapiens (human) / References: UniProt: Q8NEV9

#2: Protein

Interleukin-27 subunit beta / IL-27 subunit beta / IL-27B / Epstein-Barr virus-induced gene 3 protein / EBV-induced gene 3 protein

Mass: 23338.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Peprotech cat number 200-38 / Source: (gene. exp.)

Homo sapiens (human) / Gene: EBI3, IL27B / Cell line (production host): HEK293 / Production host:

Homo sapiens (human) / References: UniProt: Q14213

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Antibody , 2 types, 4 molecules HJIL

#3: Antibody	SRF388 Heavy Chain Mass: 24235.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO-EBNA / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody	SRF388 Light Chain Mass: 23979.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO-EBNA / Production host: Cricetulus griseus (Chinese hamster)

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Sugars / Non-polymers , 2 types, 568 molecules

#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: obtained synthetically / 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

#6: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 0.2 M ammonium citrate dibasic, 2.5 % glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 25, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.2→120.4 Å / Num. obs: 108947 / % possible obs: 99.8 % / Redundancy: 5.23 % / B_iso Wilson estimate: 45.98 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.06 / Net I/σ(I): 14.82
Reflection shell	Resolution: 2.2→2.26 Å / Redundancy: 5.34 % / Mean I/σ(I) obs: 0.92 / Num. unique obs: 8013 / CC_1/2: 0.711 / R_rim(I) all: 2.081 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
BUSTER		refinement
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6AZM,5IJK,5FUC

6azm

5ijk

5fuc

Resolution: 2.2→60.18 Å / SU ML: 0.259 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.5017
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2205	4363	5 %
R_work	0.1844	82940	-
obs	0.1862	87303	79.96 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 62.16 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→60.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12255	0	28	566	12849

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	12641
X-RAY DIFFRACTION	f_angle_d	0.5872	17207
X-RAY DIFFRACTION	f_chiral_restr	0.0424	1925
X-RAY DIFFRACTION	f_plane_restr	0.0046	2198
X-RAY DIFFRACTION	f_dihedral_angle_d	11.9355	4602

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 (%)
2.2-2.23	0.3413	37	0.2405	660	X-RAY DIFFRACTION	18.99
2.23-2.25	0.2546	44	0.2518	724	X-RAY DIFFRACTION	21.73
2.25-2.28	0.3089	38	0.245	846	X-RAY DIFFRACTION	24.33
2.28-2.31	0.2947	54	0.2609	1041	X-RAY DIFFRACTION	30.32
2.31-2.34	0.2762	71	0.26	1243	X-RAY DIFFRACTION	36.22
2.34-2.37	0.262	78	0.2503	1501	X-RAY DIFFRACTION	43.81
2.37-2.4	0.2616	82	0.2574	1736	X-RAY DIFFRACTION	50.04
2.4-2.44	0.3101	111	0.2621	2035	X-RAY DIFFRACTION	59.25
2.44-2.48	0.345	123	0.2734	2342	X-RAY DIFFRACTION	67.15
2.48-2.52	0.2831	134	0.2651	2615	X-RAY DIFFRACTION	76.17
2.52-2.56	0.2764	185	0.253	2825	X-RAY DIFFRACTION	83.1
2.56-2.61	0.2762	151	0.2377	3169	X-RAY DIFFRACTION	91.71
2.61-2.66	0.2906	162	0.2338	3342	X-RAY DIFFRACTION	96.29
2.66-2.71	0.3042	185	0.228	3453	X-RAY DIFFRACTION	99.75
2.71-2.77	0.2811	190	0.2128	3411	X-RAY DIFFRACTION	99.92
2.77-2.84	0.2282	187	0.2165	3440	X-RAY DIFFRACTION	99.92
2.84-2.91	0.2391	172	0.2186	3470	X-RAY DIFFRACTION	99.89
2.91-2.99	0.2644	171	0.222	3457	X-RAY DIFFRACTION	99.97
2.99-3.07	0.2926	166	0.2258	3454	X-RAY DIFFRACTION	99.92
3.07-3.17	0.2897	203	0.2033	3411	X-RAY DIFFRACTION	99.86
3.17-3.29	0.2062	187	0.1808	3469	X-RAY DIFFRACTION	99.86
3.29-3.42	0.2224	174	0.1809	3478	X-RAY DIFFRACTION	99.95
3.42-3.57	0.1886	200	0.1696	3418	X-RAY DIFFRACTION	99.72
3.57-3.76	0.2275	177	0.1763	3470	X-RAY DIFFRACTION	99.78
3.76-4	0.2029	180	0.1662	3446	X-RAY DIFFRACTION	99.83
4-4.31	0.1832	178	0.1412	3471	X-RAY DIFFRACTION	100
4.31-4.74	0.1588	192	0.134	3481	X-RAY DIFFRACTION	99.95
4.74-5.42	0.1891	200	0.1423	3478	X-RAY DIFFRACTION	99.95
5.42-6.83	0.2109	147	0.1918	3516	X-RAY DIFFRACTION	99.73
6.83-60.18	0.204	184	0.1881	3538	X-RAY DIFFRACTION	99.02

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	4.13353966291	-0.248264988547	1.11649900514	3.65594095301	-0.163159106812	5.36700130277	0.000565783699292	0.0813502755195	-0.108984421697	0.0968627275607	0.0249487983386	-0.506684485336	-0.0841388347718	1.16964560293	-0.0138833324952	0.351798619255	-0.104861208886	0.020480032367	0.558807259687	-0.0785694799173	0.441331051564	28.2836797656	-8.2033918792	-13.6418251373
2	3.89149933481	1.16650476539	3.05540110565	2.78093438602	1.71032492115	2.93811069824	-0.0945872912784	-0.895687523769	0.471001835397	0.28436753093	0.240075615146	-0.522846391398	-0.401906824616	1.10472779178	-0.0336033633309	0.440545351027	-0.0471197913386	-0.0253329587183	1.17749131069	-0.279541633255	0.629310430847	34.9671188793	-3.26341696876	13.4367735127
3	5.15596688944	2.85018871347	-0.406032169441	5.84481180779	-0.430510012505	5.09252834419	-0.0976134003873	-0.389436788937	-0.0632874963703	0.150839524451	0.00643658361645	0.195712387887	0.605623442955	-0.063177049186	0.0988939180351	0.328488055369	0.100549979639	0.0490409910991	0.417542233578	-0.0673916827118	0.307974697237	9.95821707762	-21.586800019	8.35934018677
4	3.45616549418	0.294518834511	1.28156731207	2.52128898919	0.407350702669	4.50830001377	0.0352661234543	-0.281961223873	-0.00337107533754	-0.000877999981354	-0.0528300829172	0.331005678656	-0.114910486623	-0.818141008247	0.0109292727766	0.29578546237	0.113565779637	0.0416885921223	0.391867818904	0.0179459139007	0.303691681849	1.33830639911	-6.35132877821	-106.621195913
5	3.43179117321	-0.578897245934	1.40512068281	2.19622316027	-0.877478483403	0.7834234232	-0.0890557764289	1.1820230016	0.423034868941	-0.66523926328	0.0451418348776	0.433570881536	-0.975633663096	-1.25531696832	0.108779665307	0.710054289965	0.300868210086	-0.0912491631071	1.17916933536	0.101726740104	0.557241601707	-4.68660699321	-0.399945093548	-133.586039937
6	5.05468942401	-2.61656306192	-0.630670477253	6.27182028923	-0.22031731749	4.36848173858	-0.0576722007928	0.226449944412	-0.27069110304	-0.177834991839	-0.0657813832182	-0.0719007135233	0.454096805213	-0.262056492154	0.118515537798	0.243650587889	-0.0818669444232	0.0410911413385	0.252308891055	-0.0390173122064	0.240613064713	18.238533853	-20.7882375137	-128.985834788
7	2.31697986749	-1.05944187636	0.793700513488	3.65609320201	-1.05468569981	2.85110580513	-0.0521962979019	-0.0216975108398	-0.0213922695393	-0.321560476196	0.133378039212	-0.171629427694	0.264840277008	0.067458521805	-0.0797271076224	0.322801248365	-0.00586025737181	0.0160322261523	0.219645460581	-0.0382102292147	0.201954333781	17.7365282532	-21.1389704331	-86.7478919432
8	0.371759096784	0.166784412358	-0.872921565951	2.38941726402	1.06624429946	5.90072945304	-0.0160130672336	-0.127694379402	-0.108149505005	0.211990963594	0.0286410192938	-0.0023555524336	0.501964848615	0.100166908512	-0.0198158316466	0.483882415185	0.182277375628	-0.000362347515755	0.42131569374	0.0181575005023	0.435579416954	25.743341504	-35.4206275202	-58.5825643625
9	2.38264539603	1.57337927017	0.549862628956	3.33370818597	0.590977596631	2.31195990924	0.0131336937288	-0.0386024576892	0.0980308615936	0.154306203462	0.0494412300872	0.0409164880133	0.161420530053	0.0484754237151	-0.0596655567622	0.335218736434	0.0432358000647	0.0439581847499	0.222274540789	0.0238949632755	0.220924821055	10.4175034788	-20.6388577721	-34.0259237686
10	3.26118753209	0.442076107509	-1.19651733915	4.2011156109	-1.04527379929	4.02905881898	0.122375802995	0.242034506511	0.114374398075	-0.290953267124	-0.0116849352896	0.0688650302366	0.16227855134	0.166682292908	-0.107545221517	0.266227715424	0.0207650243055	-0.0265157991707	0.258688397768	0.0726009632323	0.259750292108	-0.116847323772	-33.0971768633	-63.1647304123
11	1.52613562737	-0.0969889961148	1.85113074041	2.39890472588	-0.529054434877	5.68803659337	-0.107820396922	-0.110117551921	0.170825733151	0.089773805074	0.138565021734	-0.211838363536	-0.314054699149	0.162331741973	-0.0223382268449	0.339607251949	0.0247257117661	0.0169856461832	0.270832013774	-0.084975458405	0.327310260918	24.5273869329	-3.99147555031	-74.5008466907
12	2.03833546255	-1.07601856812	0.638961034183	4.86010664804	-0.998534620381	3.28544650317	-0.0872864350998	-0.209296399408	-0.159582636082	0.431343362824	0.0517456516233	-1.06596172296	0.322287514012	0.752826655822	0.0773150758024	0.501937242933	0.272622392419	-0.153202787361	0.699802124253	-0.0353917246301	0.542063533774	40.0888106269	-32.0065597916	-53.4377898335
13	1.56015026543	-0.0130993346682	1.03867522405	1.22531013794	-1.16082674836	5.03158400774	-0.118074037545	0.0332248136342	0.325137017774	0.0103015745566	0.0636818950965	0.0362805256858	-0.570907544749	-0.0158386663792	0.0621268630817	0.427212348175	-0.0143888855132	0.046687760454	0.203366393896	0.036670838824	0.39197772806	5.63297614995	-2.19257122078	-45.4432695563
14	1.54598888366	0.595435872766	0.0481401980857	5.12114460744	-0.757046825263	2.7367814943	0.0170881750865	0.104385578356	0.105605700566	-0.56970919606	0.0613100157085	1.17434175265	0.0802267965537	-0.386762460041	-0.0873569413873	0.359011882888	0.0135514006131	-0.148756890464	0.4317886734	0.114918989401	0.50863849569	-13.7244354647	-26.8878626638	-67.420203255

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain A and protein	A	A	35 - 227	1 - 160
2	2	chain B and (resid 1:127 or resid 240)	B	B - C	31 - 240	1
3	3	chain B and resid 128:230	B	B	128 - 226	82 - 180
4	4	chain C and protein	C	D	31 - 226	1 - 166
5	5	chain D and (resid 1:127 or resid 240)	D	E - F	31 - 240	1
6	6	chain D and resid 128:230	D	E	128 - 225	78 - 175
7	7	chain H and resid 1:128	H	G	1 - 128	1 - 128
8	8	chain H and resid 129:400	H	G	129 - 226	129 - 226
9	9	chain J and resid 1:128	J	I	1 - 128	1 - 128
10	10	chain J and resid 129:400	J	I	129 - 229	129 - 229
11	11	chain L and resid 1:115	L	J	1 - 115	1 - 115
12	12	chain L and resid 116:400	L	J	116 - 219	116 - 219
13	13	chain I and resid 1:115	I	H	1 - 115	1 - 115
14	14	chain I and resid 116:400	I	H	116 - 220	116 - 220

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News

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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.
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Interleukin-27 subunit ... , 2 types, 4 molecules ACBD

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Antibody , 2 types, 4 molecules HJIL

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