PDB-7srk: Single chain trimer HLA-A*24:02 (Y108C, A163C) with 8mer peptide ...

ID or keywords:

Entry

Database: PDB / ID: 7srk

Title

Single chain trimer HLA-A*24:02 (Y108C, A163C) with 8mer peptide YPPVPETF

Components

RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera
VHH

Keywords

IMMUNE SYSTEM / HLA / VHH / HPV / SCT

Function / homology

Function and homology information

antigen processing and presentation of peptide antigen via MHC class I / negative regulation of double-strand break repair via homologous recombination /

regulation of DNA repair /

replication fork / MHC class I protein complex /

single-stranded DNA binding / nuclear speck /

immune response /

RNA binding / extracellular region /

membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Pongo pygmaeus (Bornean orangutan)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Finton, K.A.K. / Rupert, P.B.

Funding support

United States, 1items

Citation

Journal: Front Immunol / Year: 2023
Title: Effects of HLA single chain trimer design on peptide presentation and stability.
Authors: Finton, K.A.K. / Rupert, P.B. / Friend, D.J. / Dinca, A. / Lovelace, E.S. / Buerger, M. / Rusnac, D.V. / Foote-McNabb, U. / Chour, W. / Heath, J.R. / Campbell, J.S. / Pierce, R.H. / Strong, R.K.

History

Deposition	Nov 8, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 23, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 31, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7srk.cif.gz	475.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7srk.ent.gz	323.8 KB	Display	PDB format
PDBx/mmJSON format	7srk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sr/7srk ftp://data.pdbj.org/pub/pdb/validation_reports/sr/7srk	HTTPS FTP

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Related structure data

Related structure data	7sqpSC 7sr0C 7sr3C 7sr4C 7sr5C 7sshC 7st3C 7stgC S: Starting model for refinement C: citing same article (ref.)
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)

Deposited unit

A: RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera

B: VHH

C: RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera

D: VHH

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

1

A: RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera

B: VHH

defined by author
Evidence: surface plasmon resonance
59.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera

D: VHH

defined by author
59.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.924, 76.072, 226.974
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera / RPA-related and RAD51-antagonist / X-chromosome Mass: 47350.027 Da / Num. of mol.: 2 / Mutation: Y108C, A163C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pongo pygmaeus (Bornean orangutan) Gene: RADX, CXorf57, B2M, HLA-A / Production host: Homo sapiens (human) References: UniProt: Q6NSI4, UniProt: P16213, UniProt: A0A411J078
#2: Antibody	VHH Mass: 12536.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.19 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES, pH 6.0, 200 mM KSCN, 18% Peg 3350

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1 Å
Detector	Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 13, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→29.83 Å / Num. obs: 42766 / % possible obs: 99.8 % / Redundancy: 9.6 % / B_iso Wilson estimate: 39.16 Å² / CC_1/2: 0.999 / Net I/σ(I): 29.5
Reflection shell	Resolution: 2.5→2.59 Å / Num. unique obs: 4213 / CC_1/2: 0.906

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Processing

Software

Name: PHENIX / Version: 1.19.1_4122 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7SQP

7sqp

Resolution: 2.5→29.83 Å / SU ML: 0.3384 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8483
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2599	2155	5.04 %
R_work	0.2285	40604	-
obs	0.2301	42759	99.92 %

Solvent computation

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

Displacement parameters

B_iso mean: 50.06 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→29.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7604	0	0	83	7687

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0018	7796
X-RAY DIFFRACTION	f_angle_d	0.4572	10604
X-RAY DIFFRACTION	f_chiral_restr	0.0397	1121
X-RAY DIFFRACTION	f_plane_restr	0.0044	1396
X-RAY DIFFRACTION	f_dihedral_angle_d	4.3698	1086

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 (%)
2.5-2.56	0.349	136	0.2983	2646	X-RAY DIFFRACTION	99.96
2.56-2.62	0.3449	150	0.2938	2669	X-RAY DIFFRACTION	100
2.62-2.69	0.3546	159	0.2761	2655	X-RAY DIFFRACTION	100
2.69-2.77	0.3153	157	0.2786	2638	X-RAY DIFFRACTION	100
2.77-2.86	0.2821	132	0.2633	2691	X-RAY DIFFRACTION	100
2.86-2.96	0.2764	156	0.2599	2662	X-RAY DIFFRACTION	100
2.96-3.08	0.3189	142	0.2612	2679	X-RAY DIFFRACTION	99.96
3.08-3.22	0.3057	142	0.2656	2704	X-RAY DIFFRACTION	100
3.22-3.39	0.3094	129	0.2478	2685	X-RAY DIFFRACTION	100
3.39-3.6	0.2889	131	0.2429	2722	X-RAY DIFFRACTION	99.89
3.6-3.88	0.2649	125	0.223	2734	X-RAY DIFFRACTION	99.97
3.88-4.27	0.2322	152	0.1985	2706	X-RAY DIFFRACTION	99.86
4.27-4.89	0.1811	147	0.1713	2738	X-RAY DIFFRACTION	99.93
4.89-6.15	0.223	167	0.1983	2758	X-RAY DIFFRACTION	99.86
6.15-29.83	0.1973	130	0.2108	2917	X-RAY DIFFRACTION	99.38

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	1.69115860847	0.153413709326	0.784882783837	1.34698899778	0.390018922159	3.51443060649	-0.0756663184846	0.520623802947	-0.00690076779994	-0.200583482778	0.0227355002116	0.0860124540248	-0.135186209502	0.198348286883	0.106737532186	0.190661222373	-0.0261044596932	-0.0288853078794	0.274434673659	-0.0276704703819	0.186087803176	3.22804239036	-14.8840715434	-31.3555356683
2	2.34167577487	0.15144913962	0.336689778844	1.6297499874	0.393983173517	1.69368565594	0.029870891102	-0.116239531671	-0.143164606701	0.269416827815	-0.0475409089873	-0.0559260831255	0.131012481084	0.0907063653067	0.0221734319373	0.278505216167	-0.00132570215949	0.00825472604255	0.205214230852	-0.0612676173007	0.246057745329	10.2575644789	-15.5491730349	-11.7824742165
3	3.79357026928	0.256172300539	2.11251416842	0.958050155821	-0.760886831086	3.77289545153	-0.648771620073	1.30117044621	0.483987367129	-0.198661881982	0.371196677525	-0.161605895004	-0.634693924805	0.684295866104	0.31241809643	0.535639555814	-0.283384767982	-0.0839640889679	0.776231601655	0.152967905156	0.324453948777	19.085188716	-4.05996588256	-36.3874228726
4	2.35498540971	1.16578037379	-0.580287747069	2.5573349164	-1.09666343149	5.67931580762	0.235666578592	0.154486815502	0.665872516774	0.320241317788	-0.258228036701	0.569233785836	-0.788081928086	-0.279758452931	-0.021186332437	0.242496383395	0.0910217622318	-0.0505520804372	0.425123096235	-0.0680024622689	0.554460632465	-29.5579597411	-16.9828644944	-30.3871356786
5	5.19151521496	0.681297799628	1.89274218489	4.9677653252	0.0190008956163	2.56632052034	-0.225697693649	1.19357654881	0.149164608777	-1.21885467553	-0.220173415482	0.699670147673	0.233295503044	-0.485894792423	-0.120787082632	0.370663342167	0.154654125433	-0.155991509136	0.778963301174	-0.0719307215438	0.448924291234	-25.8289231044	-17.0679254484	-41.250169044
6	2.89233364671	0.649284726866	-1.04981097059	2.50774711473	0.500579560731	0.896879183253	-0.094541978799	0.312093143086	0.0833259723737	-0.102529777859	-0.012042786762	0.420947563613	-0.154495474129	-0.257709684263	0.0919947466819	0.225282281468	0.0362643073738	-0.0703556698053	0.408669447182	-0.081159884232	0.281288100018	-19.9708268964	-18.3938929102	-32.7399972499
7	1.58217349882	-1.02610608273	0.532968237058	3.02790859872	-1.68335982545	2.13520143552	0.038860166353	0.224514646756	-0.321243286296	-0.181576339439	-0.0597998713958	0.297585456098	0.193694828952	-0.115775670457	-0.0283894486602	0.307285877605	-0.047422296115	0.0392725127669	0.347306406506	-0.235080039853	0.560694446721	-12.0682592435	-48.0141927	-33.7538141294
8	1.16861237401	0.242836869702	-0.04927917967	2.47769313305	-0.888693489958	1.8503657363	-0.0630707957165	0.354426864445	-0.438102259368	-0.146641582528	-0.0964722289969	0.0523595231612	0.252810137813	-0.0241456122299	0.126440023751	0.337893283073	0.0257353693282	0.00285569050594	0.403643378831	-0.220100079827	0.480206150918	-9.39547632269	-43.9807601462	-38.3280749661
9	1.15221001064	0.254681378409	-0.146124212683	2.47553909862	-0.0598191681252	2.23998206064	-0.0178176528938	0.0119666106429	-0.101250481014	0.188105601798	0.0683297994401	-0.233812758648	-0.0638921819465	-0.211016764006	0.0424577866917	0.416294359251	0.0147505320297	0.0400428348979	0.284554362718	-0.178629302721	0.556483182571	-9.2024432564	-42.8205205114	-19.955747691
10	0.0288257858084	-0.126255186439	-0.471851587926	3.73079262598	-0.117006899606	1.09231606113	-0.0390355210932	-0.189995949999	-0.345260330761	0.278924681004	-0.00816408007724	-0.157623753976	0.349115703521	0.00499111801681	0.0296530726168	0.517534937847	-0.0135991291465	0.0141452210515	0.354205750825	-0.0595414221422	0.711055162825	-6.60717062683	-59.525918975	-14.8445671647
11	0.236749908399	-1.05881702962	-0.267989563202	3.3444033749	0.0608732294175	3.26642831822	-0.395317298015	0.0939906265031	-0.225191247768	0.946705983285	0.359705660901	0.764840942266	-0.321656196967	-1.12594787814	-0.178626797322	0.404772175215	0.00472776269743	0.242933137755	0.734515444677	-0.137626435036	0.896004146811	-28.0513199288	-47.5052694231	-18.4747734434
12	2.66703451273	0.886638031184	1.59476244235	1.23814781264	0.468636762117	1.13407268765	0.0537690906699	0.705555854194	-0.150083470924	-0.239147649877	0.0319612332234	-0.121023423452	1.15518981008	-0.902656004173	0.0446526096448	0.710280659014	-0.141278930951	-0.00152141603708	0.648361685759	-0.304870172956	0.789961329743	-27.3923172277	-54.0336350013	-48.1636040518
13	0.227589984949	-0.433987455205	0.080110195861	0.498978834944	-0.805411379943	2.76073173567	0.474220717457	0.5909717137	-0.620365610418	0.0959783073243	-0.0122634864598	0.143204723851	1.00723514853	-1.05624908368	-0.306195621868	0.648361234588	-0.206548911878	-0.0956112771421	0.913333463932	-0.457886029016	0.943549686423	-28.1636639033	-55.9558542838	-45.0615544524
14	4.51994567849	-0.405103101165	-3.54567704843	9.64436618285	-1.91437603012	4.32222583291	-0.421829301237	0.579146977196	-0.444184049054	0.48575912286	0.595054949981	-0.0984827378892	-0.524277145851	-1.16722819297	-0.285306958063	0.429670520561	0.0643159965365	0.109541021442	0.844059881033	-0.223629558824	0.60938578553	11.7060503073	-38.6385260242	-58.6985214919
15	3.73418248743	-0.867231609217	3.51630599496	0.562797606722	-0.646790392428	3.45358644288	0.183319741947	-0.886990149627	-0.841699803501	0.342913919456	-0.522409893013	-1.07537839812	-0.787157735956	1.53168023975	0.213579452038	0.599909738931	-0.322378678824	-0.0347760393771	1.43660880473	0.159159980173	1.24415257212	27.0569219905	-38.016022392	-42.0948599397
16	7.33115913983	3.28278184387	3.06130052796	2.82615600124	2.96900823818	8.35866794096	0.180132759255	-1.05614376631	0.324744382169	-0.639788189197	0.077902641494	-0.348562209126	-1.05733847036	-0.494676596502	-0.650653064436	0.495248946415	0.112719008797	0.0612875142359	0.798810789558	-0.0189739445369	0.617216892824	14.2100321328	-33.9296603032	-55.090014136
17	5.26769117593	-0.688823636065	0.449924461224	5.8930447961	0.137538245069	5.71164100358	-0.945215682477	1.09390049928	-0.661028761967	0.209528304531	-0.261457994885	-0.235659609191	-0.576487557297	-0.1169148813	0.891005339758	0.338966906129	-0.143681296674	0.197623265643	0.565157750314	-0.272519628495	0.602054064264	7.18363208704	-37.0256207382	-50.6170991616
18	2.15744391451	2.29236757758	-1.12285417186	4.62785469634	-0.519478472701	1.94021912747	0.183766959126	0.174516835139	-1.37003446826	0.0566435696557	-0.456176008193	-0.665315792887	0.410238739868	-0.102039064108	0.272348807189	0.391723674637	0.0135346306847	-0.0650184316739	0.548557605992	-0.059705629928	0.86253917025	8.89205381755	-44.2438958496	-42.9141884705
19	7.90977114231	-1.61079986063	-0.501028858997	6.45152472369	-0.907459316386	3.52557306377	0.133751682584	-0.209963880102	-0.0107743485137	0.488219612785	0.169747466967	-0.345069092824	-0.245929074072	0.256915627256	-0.439542467316	0.398892564232	-0.00957044403456	-0.0024067132246	0.543608564802	-0.0946110824537	0.352754876113	6.68738894646	-32.0263978602	-41.1529613056
20	2.32687926288	-0.391176116607	1.22823285346	6.6670229901	-4.19164830335	8.01736499161	-0.461836464875	0.321753930271	0.383936259202	0.202797376733	-0.272707458161	-1.32007221006	-0.14587873759	0.357473931947	0.717392870987	0.266392304528	0.093889739948	-0.00989018998537	0.657052298933	-0.0297003476944	0.584833095507	13.2462153782	-30.2531944998	-43.0709700275
21	3.4718586857	-3.2891732027	2.54306571107	6.28230839053	-2.97242445644	8.04270626405	-0.76148067361	0.772132341337	-0.0948738132504	-0.241120351027	-0.161367052325	-0.977198051602	-0.510813602092	0.573536441269	0.461976278654	0.302580134351	-0.124727081314	0.17494718489	0.833973002414	-0.164550973179	0.520570864698	13.6349264492	-29.3843037581	-51.6530605502
22	1.71574768465	-1.45840740022	0.38747842128	1.23484985571	-0.369629443852	1.26594222508	0.674998804066	-0.0837496535292	-0.145564796999	0.113165790255	-0.244861789884	-1.38872016082	0.181145788734	0.528310821264	-0.387755722423	0.30686847966	0.0571619262608	-0.367167566607	0.714485444989	-0.080730490915	1.66054079478	21.6970186394	-39.9112486281	-37.4003111415
23	4.18170648418	0.775537898295	1.03190750559	1.90952049113	-0.928315037052	5.02060739144	0.381612795154	0.602645111263	-0.486026400388	-0.674821379416	-0.388749351545	-0.68650898806	0.317563974442	0.248711896352	-0.255354531641	0.475641031883	0.0415608779853	0.0803317129256	0.762513752883	-0.387482418735	0.522174753386	5.7109821184	-40.6155823607	-52.4903848554
24	1.42559147672	-2.26229448907	-0.0257468209576	5.12774053234	1.40796762874	2.94789622415	-0.643838643229	-0.110031147362	0.354669543524	-0.262670001736	-0.956359128645	-0.240013640213	-0.0813647015113	-0.498002914955	1.07302759156	0.285126181136	0.529574875047	0.334072244641	0.70671909816	0.104853944583	1.12510843534	22.6633029739	-43.63982588	-45.521218659

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 (resid 1 through 107 )	A	A	1 - 107	1 - 92
2	2	chain 'A' and (resid 108 through 305 )	A	A	108 - 305	93 - 268
3	3	chain 'A' and (resid 306 through 415 )	A	A	306 - 415	269 - 373
4	4	chain 'B' and (resid 3 through 19 )	B	B	3 - 19	1 - 17
5	5	chain 'B' and (resid 20 through 32 )	B	B	20 - 32	18 - 30
6	6	chain 'B' and (resid 33 through 117 )	B	B	33 - 117	31 - 115
7	7	chain 'C' and (resid 1 through 43 )	C	C	1 - 43	1 - 27
8	8	chain 'C' and (resid 44 through 155 )	C	C	44 - 155	28 - 119
9	9	chain 'C' and (resid 156 through 199 )	C	C	156 - 199	120 - 163
10	10	chain 'C' and (resid 200 through 305 )	C	C	200 - 305	164 - 269
11	11	chain 'C' and (resid 306 through 328 )	C	C	306 - 328	270 - 292
12	12	chain 'C' and (resid 329 through 362 )	C	C	329 - 362	293 - 326
13	13	chain 'C' and (resid 363 through 417 )	C	C	363 - 417	327 - 381
14	14	chain 'D' and (resid 3 through 9 )	D	D	3 - 9	1 - 7
15	15	chain 'D' and (resid 10 through 19 )	D	D	10 - 19	8 - 17
16	16	chain 'D' and (resid 20 through 29 )	D	D	20 - 29	18 - 27
17	17	chain 'D' and (resid 30 through 41 )	D	D	30 - 41	28 - 39
18	18	chain 'D' and (resid 42 through 53 )	D	D	42 - 53	40 - 51
19	19	chain 'D' and (resid 54 through 65 )	D	D	54 - 65	52 - 63
20	20	chain 'D' and (resid 66 through 74 )	D	D	66 - 74	64 - 72
21	21	chain 'D' and (resid 75 through 84 )	D	D	75 - 84	73 - 82
22	22	chain 'D' and (resid 85 through 92 )	D	D	85 - 92	83 - 90
23	23	chain 'D' and (resid 93 through 111 )	D	D	93 - 111	91 - 109
24	24	chain 'D' and (resid 112 through 116 )	D	D	112 - 116	110 - 114

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