SAXSdb — 5iqq

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

RNA-binding protein 7

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–91 Chain B； UniProt 1–91 Chain C； UniProt 1–91 Chain D； UniProt 1–91 Chain E； UniProt 1–91	Fragment：RNA recognition motif, UNP residues 1-91	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7.5；292 K；0.1 M Hepes pH 7.5, 150 mM KCl, 1.4 M tri-sodium citrate	Resolution 2.52 Å R-free 0.244

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 5IQQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2M8H RRM domain of human RBM7 Deposited 2013-05-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–94（91 aa） Fragment：unp residues 4-94	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；293.15 K；Ionic strength (raw mmCIF value) 200；Pressure ambient NMR sample composition 0.3 mM [U-99% 13C; U-99% 15N] RBM7, 20 mM BISTRIS, 4 mM beta-mercaptoethanol, 200 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5LXR Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Not recorded	SM SAMARIUM (III) ION × 3 BR BROMIDE ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane pH 6.5 0.2 M NaBr 18% (v/v) PEG3350 7% (w/v) glycerol	Resolution 2.00 Å R-free 0.229
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Not recorded	BR BROMIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350	Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–86（86 aa）	Not recorded	BR BROMIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350	Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–86（86 aa）	Not recorded	BR BROMIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350	Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–86（86 aa）	Not recorded	BR BROMIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350	Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 1–86（86 aa）	Not recorded	BR BROMIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350	Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 1–86（86 aa）	Not recorded	BR BROMIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350	Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 1–86（86 aa）	Not recorded	BR BROMIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350	Resolution 2.85 Å R-free 0.300
7S7B Human Nuclear exosome targeting (NEXT) complex homodimer bound to RNA (substrate 1) Deposited 2021-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric	Chain C 7–86（80 aa） Chain G 7–86（80 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-Cl pH 8.0, 50 mM NaCl, 0.1 mM TCEP supplemented with 0.02% (v/v) IGEPAL CA-630 cryo-EM vitrification conditions Cryogen ETHANE；30 s wait time, blot for 2.5 s before plunging	Resolution 4.06 Å
7S7C Human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2) Deposited 2021-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain C 7–86（80 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；30 s wait time, blot for 2.5 s before plunging	Resolution 3.62 Å

5 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RBM7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–91； UniProt 1–91 Author chain B； PDBConstruct 1–91； UniProt 1–91 Author chain C； PDBConstruct 1–91； UniProt 1–91 Author chain D； PDBConstruct 1–91； UniProt 1–91 Author chain E； PDBConstruct 1–91； UniProt 1–91

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	5iqq
Deposition date deposition_date	2016-03-11
Structure title title	Crystal structure of the human RBM7 RRM domain
Keywords keywords	pentameric assembly, RRM fold, non-crystallographic symmetry, RNA binding protein, NEXT complex, exosome, RNA degradation; RNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	28.56 Å
Radius of gyration Rg (electron density) rg_electron	27.37 Å
Forward intensity I(0) i0	29490600.00
Molecular weight molecular_weight	46114.0 kDa
Excluded volume excluded_volume	59487 Å³
Envelope volume envelope_volume	79748 Å³
Hydration-shell volume shell_volume	24029 Å³
Envelope diameter envelope_diameter	92.7 Å
Shell Rg shell_rg	34.96 Å
Envelope Rg envelope_rg	26.83 Å
Shape Rg shape_rg	27.33 Å
Total Rg total_rg	28.39 Å
Total atoms total_atoms	6665
Residues n_residues	405
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	87.7 Å
Rg (real space) rg_real	28.45 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	2.9490e+07
I(0) uncertainty (real space) i0_real_error	4.1120e+05
Rg (reciprocal space) rg_reciprocal	28.49 Å
I(0) (reciprocal space) i0_reciprocal	29490000.0000
Solution quality estimate total_estimate	0.9039
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.3 Å
Skewness Skewness skewness	0.083
Kurtosis Kurtosis kurtosis	-0.668
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5784000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.955

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5iqqa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.0 — automated matches

Domain ID domain_id	d5iqqb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.0 — automated matches

Domain ID domain_id	d5iqqc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.0 — automated matches

Domain ID domain_id	d5iqqd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.0 — automated matches

Domain ID domain_id	d5iqqe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id	5iqqA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5iqqB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5iqqC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5iqqD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5iqqE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

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8. Citations (1)

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Unit-cell length a length_a	115.707 Å
Unit-cell length b length_b	83.210 Å
Unit-cell length c length_c	60.826 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.520 Å
Low-resolution limit resolution_low	49.085 Å
R factor r_factor	0.2175
R_work r_work	0.2161
R_free r_free	0.2445

Description description	RNA-binding protein 7
Molecular weight formula_weight	10116.8 kDa
Source method src_method	man
Copy count entity_count	5

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	6919

Crystal structure of the human RBM7 RRM domain

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

RNA-binding protein 7

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	254

fit	/app/data/saxs_computation/iq/5iqq/5iqq.fit
pddf	/app/data/pr_computation/iq/5iqq/5iqq.pr.out
profile	/app/data/saxs_computation/iq/5iqq/5iqq.dat