2bcj

Crystal Structure of G Protein-Coupled Receptor Kinase 2 in Complex with Galpha-q and Gbetagamma Subunits

Method: X-RAY DIFFRACTION D_max: 146.7 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2bcj
沉积日期 deposition_date	2005-10-19
结构标题 title	Crystal Structure of G Protein-Coupled Receptor Kinase 2 in Complex with Galpha-q and Gbetagamma Subunits
关键词 keywords	Peripheral membrane complex, protein kinase, RGS domain, WD40 protein, heterotrimeric G protein, TRANSFERASE-HYDROLASE COMPLEX; TRANSFERASE/HYDROLASE
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	47.31 Å
回转半径 Rg (电子) rg_electron	46.94 Å
零角强度 I(0) i0	358872000.00
分子量 molecular_weight	154850.0 kDa
排除体积 excluded_volume	193220 Å³
包络体积 envelope_volume	284790 Å³
水化壳体积 shell_volume	51795 Å³
包络直径 envelope_diameter	147.0 Å
壳层 Rg shell_rg	49.79 Å
包络 Rg envelope_rg	45.33 Å
形状 Rg shape_rg	46.93 Å
总 Rg total_rg	47.11 Å
总原子数 total_atoms	10873
残基数 n_residues	1344
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	146.7 Å
Rg (实空间) rg_real	47.24 Å
Rg 误差 (实空间) rg_real_error	1.28 Å
I(0) (实空间) i0_real	3.5890e+08
I(0) 误差 (实空间) i0_real_error	6.5390e+06
Rg (倒空间) rg_reciprocal	47.31 Å
I(0) (倒空间) i0_reciprocal	358900000.0000
解质量估计 total_estimate	0.8522
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	80.0 Å
偏度 Skewness skewness	0.033
峰度 Kurtosis kurtosis	-0.963
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	26640000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.675

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (8)

Entity 1 polymer

描述 description	G-protein-coupled receptor kinase 2
分子量 formula_weight	79749.9 kDa
EC 编号 ec_number	2.7.11.15
突变 mutation	S670A
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	10878

MADLEAVLADVSYLMAMEKSKATPAARASKKILLPEPSIRSVMQKYLEDRGEVTFEKIFSQKLGYLLFRDFCLKHLEEAKPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIMKELLACSHPFSKSAIEHVQGHLVKKQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFCQWKNVELNIHLTMNDFSVHRIIGRGGFGEVYGCRKADTGKMYAMKCLDKKRIKMKQGETLALNERIMLSLVSTGDCPFIVCMSYAFHTPDKLSFILDLMNGGDLHYHLSQHGVFSEADMRFYAAEIILGLEHMHNRFVVYRDLKPANILLDEHGHVRISDLGLACDFSKKKPHASVGTHGYMAPEVLQKGVAYDSSADWFSLGCMLFKLLRGHSPFRQHKTKDKHEIDRMTLTMAVELPDSFSPELRSLLEGLLQRDVNRRLGCLGRGAQEVKESPFFRSLDWQMVFLQKYPPPLIPPRGEVNAADAFDIGSFDEEDTKGIKLLDSDQELYRNFPLTISERWQQEVAETVFDTINAETDRLEARKKTKNKQLGHEEDYALGKDCIMHGYMSKMGNPFLTQWQRRYFYLFPNRLEWRGEGEAPQSLLTMEEIQSVEETQIKERKCLLLKIRGGKQFVLQCDSDPELVQWKKELRDAYREAQQLVQRVPKMKNKPRAPVVELSKVPLIQRGSANGL

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	Bovine
NCBI 分类编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Trichoplusia ni

Entity 2 polymer

描述 description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
分子量 formula_weight	37311.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

XSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	Bovine
NCBI 分类编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Trichoplusia ni

Entity 3 polymer

描述 description	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
分子量 formula_weight	7845.1 kDa
突变 mutation	C68S
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G

MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFSAIL

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	Bovine
NCBI 分类编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Trichoplusia ni

Entity 4 polymer

描述 description	Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(q) subunit alpha chimera
分子量 formula_weight	41298.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	Q

MGCTLSAEDKAAVERSKMIDRNLREDGERSRRELKLLLLGTGESGKSTFIKQMRIIHGSGYSDEDKRGFTKLVYQNIFTAMQAMIRAMDTLKIPYKYEHNKAHAQLVREVDVEKVSAFENPYVDAIKSLWNDPGIQECYDRRREYQLSDSTKYYLNDLDRVADPSYLPTQQDVLRVRVPTTGIIEYPFDLQSVIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNSSVILFLNKKDLLEEKIMYSHLVDYFPEYDGPQRDAQAAREFILKMFVDLNPDSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Trichoplusia ni

Entity 5 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	TETRAFLUOROALUMINATE ION
分子量 formula_weight	103.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	GUANOSINE-5'-DIPHOSPHATE
分子量 formula_weight	443.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	5

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (7 domains)

结构域编号 domain_id	d2bcja1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.91 — Regulator of G-protein signaling, RGS
超家族 Superfamily superfamily	a.91.1 — Regulator of G-protein signaling, RGS
家族 Family family	a.91.1.1 — Regulator of G-protein signaling, RGS

结构域编号 domain_id	d2bcja2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.55 — PH domain-like barrel
超家族 Superfamily superfamily	b.55.1 — PH domain-like
家族 Family family	b.55.1.1 — Pleckstrin-homology domain (PH domain)

结构域编号 domain_id	d2bcja3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
家族 Family family	d.144.1.7 — Protein kinases, catalytic subunit

结构域编号 domain_id	d2bcjb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.4 — WD40 repeat-like
家族 Family family	b.69.4.1 — WD40-repeat

结构域编号 domain_id	d2bcjg_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
超家族 Superfamily superfamily	a.137.3 — Transducin (heterotrimeric G protein), gamma chain
家族 Family family	a.137.3.1 — Transducin (heterotrimeric G protein), gamma chain

结构域编号 domain_id	d2bcjq1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.66 — Transducin (alpha subunit), insertion domain
超家族 Superfamily superfamily	a.66.1 — Transducin (alpha subunit), insertion domain
家族 Family family	a.66.1.1 — Transducin (alpha subunit), insertion domain

结构域编号 domain_id	d2bcjq2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

CATH v4.4 (9 domains)

结构域编号 domain_id	2bcjA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	1270 —

结构域编号 domain_id	2bcjA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	167 — Regulator of G-protein Signalling 4; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Regulator of G-protein Signalling 4, domain 2

结构域编号 domain_id	2bcjA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	2bcjA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	2bcjA05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	29 — PH-domain like
同源超家族 H-superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

结构域编号 domain_id	2bcjB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2bcjG00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	260 — G Protein Gi Gamma 2
同源超家族 H-superfamily homologous superfamily	10 — Transducin (heterotrimeric G protein), gamma chain

结构域编号 domain_id	2bcjQ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	2bcjQ02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	400 — GI Alpha 1, domain 2-like
同源超家族 H-superfamily homologous superfamily	10 — GI Alpha 1, domain 2-like

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7. 引用文献 (1)

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晶胞边长 a length_a	64.918 Å
晶胞边长 b length_b	129.954 Å
晶胞边长 c length_c	122.764 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.81 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	3.061 Å
最低分辨率 resolution_low	46.780 Å
R 因子 r_factor	0.2360
R_work r_work	0.2430
R_free r_free	0.2920

fit	/app/data/saxs_computation/bc/2bcj/2bcj.fit
pddf	/app/data/pr_computation/bc/2bcj/2bcj.pr.out
profile	/app/data/saxs_computation/bc/2bcj/2bcj.dat

Crystal Structure of G Protein-Coupled Receptor Kinase 2 in Complex with Galpha-q and Gbetagamma Subunits

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (8)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (7 domains)

CATH v4.4 (9 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)