1smy

Structural basis for transcription regulation by alarmone ppGpp

Method: X-RAY DIFFRACTION

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

DNA-directed RNA polymerase alpha chain

物种未注明

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	蛋白异源复合物	异源复合物	蛋白 6	DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） RNA POLYMERASE OMEGA SUBUNIT × 1 principal sigma factor × 1 MAGNESIUM ION × 359 ZINC ION × 2 water × 6	与蛋白数一致
2	蛋白异源复合物	异源复合物	蛋白 6	DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） RNA POLYMERASE OMEGA SUBUNIT × 1 principal sigma factor × 1 MAGNESIUM ION × 3 ZINC ION × 2 GUANOSINE-5',3'-TETRAPHOSPHATE × 2 water × 6	与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	RPOA_THETH
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–315； UniProt 1–315 作者链 B； PDB构建体 1–315； UniProt 1–315 作者链 K； PDB构建体 1–315； UniProt 1–315 作者链 L； PDB构建体 1–315； UniProt 1–315

DNA-directed RNA polymerase beta chain

物种未注明

UniProt Q8RQE9

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	蛋白异源复合物	异源复合物	蛋白 6	DNA-directed RNA polymerase alpha chain × 2 （Q9Z9H6） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） RNA POLYMERASE OMEGA SUBUNIT × 1 principal sigma factor × 1 MAGNESIUM ION × 359 ZINC ION × 2 water × 6	与蛋白数一致
2	蛋白异源复合物	异源复合物	蛋白 6	DNA-directed RNA polymerase alpha chain × 2 （Q9Z9H6） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） RNA POLYMERASE OMEGA SUBUNIT × 1 principal sigma factor × 1 MAGNESIUM ION × 3 ZINC ION × 2 GUANOSINE-5',3'-TETRAPHOSPHATE × 2 water × 6	与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	RPOB_THETH
Isoform	—
PDB实体	2
链与序列区间	作者链 C； PDB构建体 1–1119； UniProt 1–1119 作者链 M； PDB构建体 1–1119； UniProt 1–1119

;DNA-directed RNA polymerase beta' chain ;

物种未注明

UniProt Q8RQE8

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	蛋白异源复合物	异源复合物	蛋白 6	DNA-directed RNA polymerase alpha chain × 2 （Q9Z9H6） DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） RNA POLYMERASE OMEGA SUBUNIT × 1 principal sigma factor × 1 MAGNESIUM ION × 359 ZINC ION × 2 water × 6	与蛋白数一致
2	蛋白异源复合物	异源复合物	蛋白 6	DNA-directed RNA polymerase alpha chain × 2 （Q9Z9H6） DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） RNA POLYMERASE OMEGA SUBUNIT × 1 principal sigma factor × 1 MAGNESIUM ION × 3 ZINC ION × 2 GUANOSINE-5',3'-TETRAPHOSPHATE × 2 water × 6	与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	RPOC_THETH
Isoform	—
PDB实体	3
链与序列区间	作者链 D； PDB构建体 1–1524； UniProt 1–1524 作者链 N； PDB构建体 1–1524； UniProt 1–1524

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	1smy
沉积日期 deposition_date	2004-03-10
结构标题 title	Structural basis for transcription regulation by alarmone ppGpp
关键词 keywords	;RNA POLYMERASE HOLOENZYME, Guanosine-tetraphosphate, ppGpp, transcription regulation, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, TRANSFERASE ;; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

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3. Official assembly/model 理论 SAXS Official SAXS Profiles

页面只读取最新 assembly 计算结果。每一条曲线都对应明确的 PDB、official biological assembly 和 coordinate model。

1smy__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

1smy__assembly_1__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

1smy__assembly_1__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	50.56 Å
Rg（电子密度）	50.19 Å
总 Rg	50.46 Å
原子数	27137
残基数	3409
排除体积	485900 Å³
最大 q	0.500 Å⁻¹

Assembly	Model	结构单元	聚集说明	状态	CRYSOL	操作
1	1	`1smy__assembly_1__model_1`	hexameric （6）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`1smy__assembly_2__model_1`	hexameric （6）	成功	4.1.3-1-20251215 (887e7ef)	查看下载

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

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5. 实体与聚合物信息 Entities & Polymers (9)

实体 1 Entity 1 polymer

描述 description	DNA-directed RNA polymerase alpha chain
分子量 formula_weight	35056.2 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,K,L
原子数 atom_count	63021

MLDSKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRINAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLKE

实体 2 Entity 2 polymer

描述 description	DNA-directed RNA polymerase beta chain
分子量 formula_weight	125436.5 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	C,M

MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGGVVTDEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKR

实体 3 Entity 3 polymer

描述 description	;DNA-directed RNA polymerase beta' chain ;
分子量 formula_weight	170997.4 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	D,N

MKKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFRAEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMNVVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEAKERPAARRGVKREQPGKQA

实体 4 Entity 4 polymer

描述 description	RNA POLYMERASE OMEGA SUBUNIT
分子量 formula_weight	11521.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	E,O

MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVFGENLVPEDRLQKEMERIYPGEREE

实体 5 Entity 5 polymer

描述 description	principal sigma factor
分子量 formula_weight	48568.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	F,P

MKKSKRKNAQAQEAQETEVLVQEEAEELPEFPEGEPDPDLEDPDLALEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD

实体 6 Entity 6 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	362

实体 7 Entity 7 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 8 Entity 8 non-polymer

描述 description	GUANOSINE-5',3'-TETRAPHOSPHATE
分子量 formula_weight	603.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 9 Entity 9 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	9031

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6. 折叠分类 (SCOP + CATH) 56 domains

SCOP 2.08 (20 domains)

结构域编号 domain_id	d1smya1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.74 — DCoH-like
超家族 Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
家族 Family family	d.74.3.1 — RNA polymerase alpha subunit dimerisation domain

结构域编号 domain_id	d1smya2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.181 — Insert subdomain of RNA polymerase alpha subunit
超家族 Superfamily superfamily	d.181.1 — Insert subdomain of RNA polymerase alpha subunit
家族 Family family	d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit

结构域编号 domain_id	d1smyb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.74 — DCoH-like
超家族 Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
家族 Family family	d.74.3.1 — RNA polymerase alpha subunit dimerisation domain

结构域编号 domain_id	d1smyb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.181 — Insert subdomain of RNA polymerase alpha subunit
超家族 Superfamily superfamily	d.181.1 — Insert subdomain of RNA polymerase alpha subunit
家族 Family family	d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit

结构域编号 domain_id	d1smyc_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
超家族 Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
家族 Family family	e.29.1.1 — RNA-polymerase beta

结构域编号 domain_id	d1smyd_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
超家族 Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
家族 Family family	e.29.1.2 — RNA-polymerase beta-prime

结构域编号 domain_id	d1smye_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.143 — RPB6/omega subunit-like
超家族 Superfamily superfamily	a.143.1 — RPB6/omega subunit-like
家族 Family family	a.143.1.1 — RNA polymerase omega subunit

结构域编号 domain_id	d1smyf1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
家族 Family family	a.4.13.1 — Sigma3 domain

结构域编号 domain_id	d1smyf2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
家族 Family family	a.4.13.2 — Sigma4 domain

结构域编号 domain_id	d1smyf3
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.177 — Sigma2 domain of RNA polymerase sigma factors
超家族 Superfamily superfamily	a.177.1 — Sigma2 domain of RNA polymerase sigma factors
家族 Family family	a.177.1.1 — Sigma2 domain of RNA polymerase sigma factors

结构域编号 domain_id	d1smyk1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.74 — DCoH-like
超家族 Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
家族 Family family	d.74.3.1 — RNA polymerase alpha subunit dimerisation domain

结构域编号 domain_id	d1smyk2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.181 — Insert subdomain of RNA polymerase alpha subunit
超家族 Superfamily superfamily	d.181.1 — Insert subdomain of RNA polymerase alpha subunit
家族 Family family	d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit

结构域编号 domain_id	d1smyl1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.74 — DCoH-like
超家族 Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
家族 Family family	d.74.3.1 — RNA polymerase alpha subunit dimerisation domain

结构域编号 domain_id	d1smyl2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.181 — Insert subdomain of RNA polymerase alpha subunit
超家族 Superfamily superfamily	d.181.1 — Insert subdomain of RNA polymerase alpha subunit
家族 Family family	d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit

结构域编号 domain_id	d1smym_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
超家族 Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
家族 Family family	e.29.1.1 — RNA-polymerase beta

结构域编号 domain_id	d1smyn_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
超家族 Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
家族 Family family	e.29.1.2 — RNA-polymerase beta-prime

结构域编号 domain_id	d1smyo_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.143 — RPB6/omega subunit-like
超家族 Superfamily superfamily	a.143.1 — RPB6/omega subunit-like
家族 Family family	a.143.1.1 — RNA polymerase omega subunit

结构域编号 domain_id	d1smyp1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
家族 Family family	a.4.13.1 — Sigma3 domain

结构域编号 domain_id	d1smyp2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
家族 Family family	a.4.13.2 — Sigma4 domain

结构域编号 domain_id	d1smyp3
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.177 — Sigma2 domain of RNA polymerase sigma factors
超家族 Superfamily superfamily	a.177.1 — Sigma2 domain of RNA polymerase sigma factors
家族 Family family	a.177.1.1 — Sigma2 domain of RNA polymerase sigma factors

CATH v4.4 (36 domains)

结构域编号 domain_id	1smyA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

结构域编号 domain_id	1smyA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

结构域编号 domain_id	1smyB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

结构域编号 domain_id	1smyB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

结构域编号 domain_id	1smyC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	270 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
同源超家族 H-superfamily homologous superfamily	10 — DNA-directed RNA polymerase, subunit 2, domain 6

结构域编号 domain_id	1smyC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1100 — Rna Polymerase Beta Subunit; Chain: C,domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1smyC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase Rpb2, domain 2

结构域编号 domain_id	1smyC04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	150 — Rna Polymerase Beta Subunit; Chain: C, domain 4
同源超家族 H-superfamily homologous superfamily	10 — DNA-directed RNA polymerase, beta subunit, external 1 domain

结构域编号 domain_id	1smyC05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

结构域编号 domain_id	1smyC06
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

结构域编号 domain_id	1smyD03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

结构域编号 domain_id	1smyD04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1smyD05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase Rpb1, domain 3

结构域编号 domain_id	1smyD06
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	132 — Topoisomerase I; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	30 — RNA polymerase Rpb1 funnel domain

结构域编号 domain_id	1smyE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	940 — Eukaryotic RPB6 RNA polymerase subunit
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase subunit, RPB6/omega

结构域编号 domain_id	1smyF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	1810 —

结构域编号 domain_id	1smyF02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1smyF03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1smyK01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

结构域编号 domain_id	1smyK02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

结构域编号 domain_id	1smyL01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

结构域编号 domain_id	1smyL02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

结构域编号 domain_id	1smyM01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	270 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
同源超家族 H-superfamily homologous superfamily	10 — DNA-directed RNA polymerase, subunit 2, domain 6

结构域编号 domain_id	1smyM02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1100 — Rna Polymerase Beta Subunit; Chain: C,domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1smyM03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase Rpb2, domain 2

结构域编号 domain_id	1smyM04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	150 — Rna Polymerase Beta Subunit; Chain: C, domain 4
同源超家族 H-superfamily homologous superfamily	10 — DNA-directed RNA polymerase, beta subunit, external 1 domain

结构域编号 domain_id	1smyM05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

结构域编号 domain_id	1smyM06
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

结构域编号 domain_id	1smyN03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

结构域编号 domain_id	1smyN04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1smyN05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase Rpb1, domain 3

结构域编号 domain_id	1smyN06
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	132 — Topoisomerase I; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	30 — RNA polymerase Rpb1 funnel domain

结构域编号 domain_id	1smyO00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	940 — Eukaryotic RPB6 RNA polymerase subunit
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase subunit, RPB6/omega

结构域编号 domain_id	1smyP01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	1810 —

结构域编号 domain_id	1smyP02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1smyP03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

▶

晶胞边长 a length_a	236.350 Å
晶胞边长 b length_b	236.350 Å
晶胞边长 c length_c	249.040 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 32
空间群编号 int_tables_number	145
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2660
R_work r_work	0.1860
R_free r_free	0.2660

Structural basis for transcription regulation by alarmone ppGpp

1. 蛋白身份与相关结构 Protein Identity & Related Structures

DNA-directed RNA polymerase alpha chain

当前结构中的状态

数据库中的同蛋白其他状态

DNA-directed RNA polymerase beta chain

当前结构中的状态

数据库中的同蛋白其他状态

;DNA-directed RNA polymerase beta' chain ;

当前结构中的状态

数据库中的同蛋白其他状态

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

1smy__assembly_1__model_1

1smy__assembly_1__model_1 | I(q)

1smy__assembly_1__model_1 | P(r) · Pending

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. 实体与聚合物信息 Entities & Polymers (9)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 polymer

聚合物 Polymer

实体 4 Entity 4 polymer

聚合物 Polymer

实体 5 Entity 5 polymer

聚合物 Polymer

实体 6 Entity 6 non-polymer

实体 7 Entity 7 non-polymer

实体 8 Entity 8 non-polymer

实体 9 Entity 9 water

6. 折叠分类 (SCOP + CATH) 56 domains

SCOP 2.08 (20 domains)

CATH v4.4 (36 domains)

7. 引用文献 (1)

Structural basis for transcription regulation by alarmone ppGpp

1. 蛋白身份与相关结构 Protein Identity & Related Structures

DNA-directed RNA polymerase alpha chain

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

DNA-directed RNA polymerase beta chain

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

;DNA-directed RNA polymerase beta' chain ;

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

1smy__assembly_1__model_1

1smy__assembly_1__model_1 | I(q)

1smy__assembly_1__model_1 | P(r) · Pending

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. 实体与聚合物信息 Entities & Polymers (9)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 polymer

聚合物 Polymer

实体 4 Entity 4 polymer

聚合物 Polymer

实体 5 Entity 5 polymer

聚合物 Polymer

实体 6 Entity 6 non-polymer

实体 7 Entity 7 non-polymer

实体 8 Entity 8 non-polymer

实体 9 Entity 9 water

6. 折叠分类 (SCOP + CATH) 56 domains

SCOP 2.08 (20 domains)

CATH v4.4 (36 domains)

7. 引用文献 (1)