SAXSdb — 8xmk

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Scavenger receptor cysteine-rich type 1 protein M130

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 42–1050 Chain E； UniProt 42–1050 Chain F； UniProt 42–1050	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 17	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.03 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8XMK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8XMP Structure of CD163 in complex with Hb-Hp Deposited 2023-12-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 42–1050（1009 aa） Chain E 42–1050（1009 aa） Chain F 42–1050（1009 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CA CALCIUM ION × 23 HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
8XMQ Structure of dimeric CD163 in complex with Hb-Hp Deposited 2023-12-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 42–1050（1009 aa） Chain F 42–1050（1009 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 CA CALCIUM ION × 12 HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
8XMW Local refinement of Hb-Hp bind to CD163 Deposited 2023-12-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 42–1050（1009 aa） Chain G 42–1050（1009 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 6 HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
9FHB Cryo-EM structure of human CD163 SRCR2-4 in complex with haptoglobin-hemoglobin Deposited 2024-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–1156（1156 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.87 Å
9FMU Cryo-EM structure of human CD163 SRCR1-9 in complex with haptoglobin-hemoglobin Deposited 2024-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–1036（1036 aa） Chain E 1–1036（1036 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.46 Å
9FNO Cryo-EM structure of human CD163 SRCR1-9 in complex with haptoglobin-hemoglobin Deposited 2024-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain E 1–1156（1156 aa） Chain F 1–1156（1156 aa） Chain G 1–1156（1156 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.20 Å
9HEJ Dimeric CD163 bound to human haptoglobin-haemoglobin complex Deposited 2024-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–1156（1156 aa） Chain B 1–1156（1156 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 9 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.82 Å
9HEK Trimeric CD163 bound to human haptoglobin-haemoglobin complex Deposited 2024-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–1156（1156 aa） Chain B 1–1156（1156 aa） Chain C 1–1156（1156 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 19 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9HEL Unliganded dimeric CD163 with arm-arm contacts Deposited 2024-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–1156（1156 aa） Chain B 1–1156（1156 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9NB5 Cryo-EM structure of the autoinhibitory CD163 trimer Deposited 2025-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 42–1045（1004 aa） Chain B 42–1045（1004 aa） Chain C 42–1045（1004 aa）	Not recorded	CA CALCIUM ION × 20 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9NB6 Cryo-EM structure of the CD163/Hp(1-1)Hb complex Deposited 2025-02-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 42–1045（1004 aa） Chain B 42–1045（1004 aa） Chain C 42–1045（1004 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 CA CALCIUM ION × 23 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9NB8 Cryo-EM structure of the CD163/HpSPHb complex Deposited 2025-02-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 42–1045（1004 aa） Chain B 42–1045（1004 aa） Chain C 42–1045（1004 aa）	Not recorded	CA CALCIUM ION × 21 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
9TQD CD163 bound to haemoglobin Deposited 2025-12-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–1156（1156 aa） Chain B 1–1156（1156 aa） Chain C 1–1156（1156 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CA CALCIUM ION × 16 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 OXY OXYGEN MOLECULE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C163A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain D； PDBConstruct 1–1009； UniProt 42–1050 Author chain E； PDBConstruct 1–1009； UniProt 42–1050 Author chain F； PDBConstruct 1–1009； UniProt 42–1050

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8xmk
Deposition date deposition_date	2023-12-27
Structure title title	Local refinement of SRCR5-9 domains
Keywords keywords	Homotrimer, receptor, ENDOCYTOSIS; ENDOCYTOSIS
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	45.95 Å
Radius of gyration Rg (electron density) rg_electron	45.52 Å
Forward intensity I(0) i0	496420000.00
Molecular weight molecular_weight	169670.0 kDa
Excluded volume excluded_volume	206080 Å³
Envelope volume envelope_volume	314920 Å³
Hydration-shell volume shell_volume	57042 Å³
Envelope diameter envelope_diameter	134.3 Å
Shell Rg shell_rg	52.74 Å
Envelope Rg envelope_rg	42.67 Å
Shape Rg shape_rg	45.52 Å
Total Rg total_rg	45.83 Å
Total atoms total_atoms	11815
Residues n_residues	1553
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	133.2 Å
Rg (real space) rg_real	45.71 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	4.9640e+08
I(0) uncertainty (real space) i0_real_error	8.4730e+06
Rg (reciprocal space) rg_reciprocal	45.95 Å
I(0) (reciprocal space) i0_reciprocal	496600000.0000
Solution quality estimate total_estimate	0.8710
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	74.4 Å
Skewness Skewness skewness	-0.068
Kurtosis Kurtosis kurtosis	-0.906
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17130000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.449

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Scavenger receptor cysteine-rich type 1 protein M130
Molecular weight formula_weight	109172.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F
Atom count atom_count	11815

SSLGGTDKELRLVDGENKCSGRVEVKVQEEWGTVCNNGWSMEAVSVICNQLGCPTAIKAPGWANSSAGSGRIWMDHVSCRGNESALWDCKHDGWGKHSNCTHQQDAGVTCSDGSNLEMRLTRGGNMCSGRIEIKFQGRWGTVCDDNFNIDHASVICRQLECGSAVSFSGSSNFGEGSGPIWFDDLICNGNESALWNCKHQGWGKHNCDHAEDAGVICSKGADLSLRLVDGVTECSGRLEVRFQGEWGTICDDGWDSYDAAVACKQLGCPTAVTAIGRVNASKGFGHIWLDSVSCQGHEPAIWQCKHHEWGKHYCNHNEDAGVTCSDGSDLELRLRGGGSRCAGTVEVEIQRLLGKVCDRGWGLKEADVVCRQLGCGSALKTSYQVYSKIQATNTWLFLSSCNGNETSLWDCKNWQWGGLTCDHYEEAKITCSAHREPRLVGGDIPCSGRVEVKHGDTWGSICDSDFSLEAASVLCRELQCGTVVSILGGAHFGEGNGQIWAEEFQCEGHESHLSLCPVAPRPEGTCSHSRDVGVVCSRYTEIRLVNGKTPCEGRVELKTLGAWGSLCNSHWDIEDAHVLCQQLKCGVALSTPGGARFGKGNGQIWRHMFHCTGTEQHMGDCPVTALGASLCPSEQVASVICSGNQSQTLSSCNSSSLGPTRPTIPEESAVACIESGQLRLVNGGGRCAGRVEIYHEGSWGTICDDSWDLSDAHVVCRQLGCGEAINATGSAHFGEGTGPIWLDEMKCNGKESRIWQCHSHGWGQQNCRHKEDAGVICSEFMSLRLTSEASREACAGRLEVFYNGAWGTVGKSSMSETTVGVVCRQLGCADKGKINPASLDKAMSIPMWVDNVQCPKGPDTLWQCPSSPWEKRLASPSEETWITCDNKIRLQEGPTSCSGRVEIWHGGSWGTVCDDSWDLDDAQVVCQQLGCGPALKAFKEAEFGQGTGPIWLNEVKCKGNESSLWDCPARRWGHSECGHKEDAAVNCTDISVQKTPQKATTGRSSRQSS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	17

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.03 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	432933

fit	/app/data/saxs_computation/xm/8xmk/8xmk.fit
pddf	/app/data/pr_computation/xm/8xmk/8xmk.pr.out
profile	/app/data/saxs_computation/xm/8xmk/8xmk.dat

Local refinement of SRCR5-9 domains

1. Protein Identity and Related Structures Protein Identity & Related Structures

Scavenger receptor cysteine-rich type 1 protein M130

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D