6N1D

X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid State


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.271 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.

Zhou, J.Lancaster, L.Donohue, J.P.Noller, H.F.

(2019) Proc Natl Acad Sci U S A 116: 7813-7818

  • DOI: https://doi.org/10.1073/pnas.1901310116
  • Primary Citation of Related Structures:  
    6N1D

  • PubMed Abstract: 

    The elongation factor G (EF-G)-catalyzed translocation of mRNA and tRNA through the ribosome is essential for vacating the ribosomal A site for the next incoming aminoacyl-tRNA, while precisely maintaining the translational reading frame. Here, the 3.2-Å crystal structure of a ribosome translocation intermediate complex containing mRNA and two tRNAs, formed in the absence of EF-G or GTP, provides insight into the respective roles of EF-G and the ribosome in translocation. Unexpectedly, the head domain of the 30S subunit is rotated by 21°, creating a ribosomal conformation closely resembling the two-tRNA chimeric hybrid state that was previously observed only in the presence of bound EF-G. The two tRNAs have moved spontaneously from their A/A and P/P binding states into ap/P and pe/E states, in which their anticodon loops are bound between the 30S body domain and its rotated head domain, while their acceptor ends have moved fully into the 50S P and E sites, respectively. Remarkably, the A-site tRNA translocates fully into the classical P-site position. Although the mRNA also undergoes movement, codon-anticodon interaction is disrupted in the absence of EF-G, resulting in slippage of the translational reading frame. We conclude that, although movement of both tRNAs and mRNA (along with rotation of the 30S head domain) can occur in the absence of EF-G and GTP, EF-G is essential for enforcing coupled movement of the tRNAs and their mRNA codons to maintain the reading frame.


  • Organizational Affiliation

    Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1D [auth AL01],
HB [auth BL01]
228Thermus thermophilusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2E [auth AL02],
IB [auth BL02]
276Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3F [auth AL03],
JB [auth BL03]
206Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4G [auth AL04],
KB [auth BL04]
205Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5H [auth AL05],
LB [auth BL05]
181Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6I [auth AL06],
MB [auth BL06]
180Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9J [auth AL09],
NB [auth BL09]
148Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13K [auth AL13],
OB [auth BL13]
140Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14L [auth AL14],
PB [auth BL14]
122Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15M [auth AL15],
QB [auth BL15]
150Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16N [auth AL16],
RB [auth BL16]
141Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17O [auth AL17],
SB [auth BL17]
118Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18P [auth AL18],
TB [auth BL18]
111Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19Q [auth AL19],
UB [auth BL19]
146Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20R [auth AL20],
VB [auth BL20]
118Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21S [auth AL21],
WB [auth BL21]
101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22T [auth AL22],
XB [auth BL22]
113Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23U [auth AL23],
YB [auth BL23]
96Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24V [auth AL24],
ZB [auth BL24]
110Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25AC [auth BL25],
W [auth AL25]
206Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27BC [auth BL27],
X [auth AL27]
84Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28CC [auth BL28],
Y [auth AL28]
98Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29DC [auth BL29],
Z [auth AL29]
72Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AA [auth AL30],
EC [auth BL30]
60Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31BA [auth AL31],
FC [auth BL31]
71Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32CA [auth AL32],
GC [auth BL32]
59Thermus thermophilusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33DA [auth AL33],
HC [auth BL33]
54Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34EA [auth AL34],
IC [auth BL34]
49Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35FA [auth AL35],
JC [auth BL35]
64Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36GA [auth AL36],
KC [auth BL36]
37Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2JA [auth AS02],
NC [auth BS02]
255Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3KA [auth AS03],
OC [auth BS03]
238Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4LA [auth AS04],
PC [auth BS04]
208Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5MA [auth AS05],
QC [auth BS05]
161Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6NA [auth AS06],
RC [auth BS06]
101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7OA [auth AS07],
SC [auth BS07]
155Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8PA [auth AS08],
TC [auth BS08]
138Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9QA [auth AS09],
UC [auth BS09]
128Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10RA [auth AS10],
VC [auth BS10]
104Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11SA [auth AS11],
WC [auth BS11]
128Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12TA [auth AS12],
XC [auth BS12]
131Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13UA [auth AS13],
YC [auth BS13]
125Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZVA [auth AS14],
ZC [auth BS14]
60Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15AD [auth BS15],
WA [auth AS15]
88Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16BD [auth BS16],
XA [auth AS16]
88Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17CD [auth BS17],
YA [auth AS17]
104Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18DD [auth BS18],
ZA [auth AS18]
87Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19AB [auth AS19],
ED [auth BS19]
92Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20BB [auth AS20],
FD [auth BS20]
105Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxCB [auth ATHX],
GD [auth BTHX]
26Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth A16S],
DB [auth B16S]
1,518Thermus thermophilus HB27
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Entity ID: 2
MoleculeChains LengthOrganismImage
23S rRNAB [auth A23S],
EB [auth B23S]
2,881Thermus thermophilus HB27
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Entity ID: 3
MoleculeChains LengthOrganismImage
5s rRNAC [auth A5S],
FB [auth B5S]
119Thermus thermophilus HB27
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Entity ID: 34
MoleculeChains LengthOrganismImage
mRNAHA [auth AMRN],
LC [auth BMRN]
17synthetic construct
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Entity ID: 35
MoleculeChains LengthOrganismImage
P-tRNAIA [auth APTN],
MC [auth BPTN]
76Escherichia coli
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Entity ID: 56
MoleculeChains LengthOrganismImage
A tRNAGB [auth BATN]85Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AR [auth BS04],
PI [auth AS04]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth A16S]
AF [auth A23S]
AG [auth A23S]
AH [auth A23S]
AI [auth AL21]
AE [auth A16S],
AF [auth A23S],
AG [auth A23S],
AH [auth A23S],
AI [auth AL21],
AJ [auth B16S],
AK [auth B23S],
AL [auth B23S],
AM [auth B23S],
AN [auth B23S],
AO [auth B23S],
AP [auth B23S],
AQ [auth BL19],
BE [auth A16S],
BF [auth A23S],
BG [auth A23S],
BH [auth A23S],
BI [auth AL21],
BJ [auth B16S],
BK [auth B23S],
BL [auth B23S],
BM [auth B23S],
BN [auth B23S],
BO [auth B23S],
BP [auth B23S],
BQ [auth BL19],
BR [auth BS16],
CE [auth A16S],
CF [auth A23S],
CG [auth A23S],
CH [auth A23S],
CI [auth AL21],
CJ [auth B16S],
CK [auth B23S],
CL [auth B23S],
CM [auth B23S],
CN [auth B23S],
CO [auth B23S],
CP [auth B5S],
CQ [auth BL20],
CR [auth BS17],
DE [auth A16S],
DF [auth A23S],
DG [auth A23S],
DH [auth A23S],
DI [auth AL23],
DJ [auth B16S],
DK [auth B23S],
DL [auth B23S],
DM [auth B23S],
DN [auth B23S],
DO [auth B23S],
DP [auth B5S],
DQ [auth BL21],
DR [auth BTHX],
EE [auth A16S],
EF [auth A23S],
EG [auth A23S],
EH [auth A23S],
EI [auth AL23],
EJ [auth B16S],
EK [auth B23S],
EL [auth B23S],
EM [auth B23S],
EN [auth B23S],
EO [auth B23S],
EP [auth B5S],
EQ [auth BL22],
FE [auth A16S],
FF [auth A23S],
FG [auth A23S],
FH [auth A23S],
FI [auth AL24],
FJ [auth B16S],
FK [auth B23S],
FL [auth B23S],
FM [auth B23S],
FN [auth B23S],
FO [auth B23S],
FP [auth B5S],
FQ [auth BL23],
GE [auth A16S],
GF [auth A23S],
GG [auth A23S],
GH [auth A23S],
GI [auth AL27],
GJ [auth B16S],
GK [auth B23S],
GL [auth B23S],
GM [auth B23S],
GN [auth B23S],
GO [auth B23S],
GP [auth B5S],
GQ [auth BL24],
HD [auth A16S],
HE [auth A16S],
HF [auth A23S],
HG [auth A23S],
HH [auth A23S],
HI [auth AL28],
HJ [auth B16S],
HK [auth B23S],
HL [auth B23S],
HM [auth B23S],
HN [auth B23S],
HO [auth B23S],
HP [auth BATN],
HQ [auth BL24],
ID [auth A16S],
IE [auth A16S],
IF [auth A23S],
IG [auth A23S],
IH [auth A23S],
II [auth AL28],
IJ [auth B16S],
IK [auth B23S],
IL [auth B23S],
IM [auth B23S],
IN [auth B23S],
IO [auth B23S],
IP [auth BL01],
IQ [auth BL25],
JD [auth A16S],
JE [auth A16S],
JF [auth A23S],
JG [auth A23S],
JH [auth A5S],
JI [auth AL33],
JJ [auth B16S],
JK [auth B23S],
JL [auth B23S],
JM [auth B23S],
JN [auth B23S],
JO [auth B23S],
JP [auth BL01],
JQ [auth BL28],
KD [auth A16S],
KE [auth A16S],
KF [auth A23S],
KG [auth A23S],
KH [auth A5S],
KI [auth AL33],
KJ [auth B16S],
KK [auth B23S],
KL [auth B23S],
KM [auth B23S],
KN [auth B23S],
KO [auth B23S],
KP [auth BL02],
KQ [auth BL28],
LD [auth A16S],
LE [auth A16S],
LF [auth A23S],
LG [auth A23S],
LH [auth A5S],
LI [auth AL33],
LJ [auth B16S],
LK [auth B23S],
LL [auth B23S],
LM [auth B23S],
LN [auth B23S],
LO [auth B23S],
LP [auth BL02],
LQ [auth BL29],
MD [auth A16S],
ME [auth A16S],
MF [auth A23S],
MG [auth A23S],
MH [auth AL01],
MI [auth AL34],
MJ [auth B16S],
MK [auth B23S],
ML [auth B23S],
MM [auth B23S],
MN [auth B23S],
MO [auth B23S],
MP [auth BL02],
MQ [auth BL29],
ND [auth A16S],
NE [auth A16S],
NF [auth A23S],
NG [auth A23S],
NH [auth AL01],
NI [auth AS02],
NJ [auth B16S],
NK [auth B23S],
NL [auth B23S],
NM [auth B23S],
NN [auth B23S],
NO [auth B23S],
NP [auth BL02],
NQ [auth BL29],
OD [auth A16S],
OE [auth A23S],
OF [auth A23S],
OG [auth A23S],
OH [auth AL02],
OI [auth AS03],
OJ [auth B16S],
OK [auth B23S],
OL [auth B23S],
OM [auth B23S],
ON [auth B23S],
OO [auth B23S],
OP [auth BL02],
OQ [auth BL29],
PD [auth A16S],
PE [auth A23S],
PF [auth A23S],
PG [auth A23S],
PH [auth AL02],
PJ [auth B16S],
PK [auth B23S],
PL [auth B23S],
PM [auth B23S],
PN [auth B23S],
PO [auth B23S],
PP [auth BL03],
PQ [auth BL29],
QD [auth A16S],
QE [auth A23S],
QF [auth A23S],
QG [auth A23S],
QH [auth AL04],
QI [auth AS06],
QJ [auth B16S],
QK [auth B23S],
QL [auth B23S],
QM [auth B23S],
QN [auth B23S],
QO [auth B23S],
QP [auth BL04],
QQ [auth BL30],
RD [auth A16S],
RE [auth A23S],
RF [auth A23S],
RG [auth A23S],
RH [auth AL04],
RI [auth AS06],
RJ [auth B16S],
RK [auth B23S],
RL [auth B23S],
RM [auth B23S],
RN [auth B23S],
RO [auth B23S],
RP [auth BL15],
RQ [auth BL31],
SD [auth A16S],
SE [auth A23S],
SF [auth A23S],
SG [auth A23S],
SH [auth AL04],
SI [auth AS08],
SJ [auth B16S],
SK [auth B23S],
SL [auth B23S],
SM [auth B23S],
SN [auth B23S],
SO [auth B23S],
SP [auth BL15],
SQ [auth BL32],
TD [auth A16S],
TE [auth A23S],
TF [auth A23S],
TG [auth A23S],
TH [auth AL06],
TI [auth B16S],
TJ [auth B16S],
TK [auth B23S],
TL [auth B23S],
TM [auth B23S],
TN [auth B23S],
TO [auth B23S],
TP [auth BL15],
TQ [auth BL33],
UD [auth A16S],
UE [auth A23S],
UF [auth A23S],
UG [auth A23S],
UH [auth AL14],
UI [auth B16S],
UJ [auth B16S],
UK [auth B23S],
UL [auth B23S],
UM [auth B23S],
UN [auth B23S],
UO [auth B23S],
UP [auth BL16],
UQ [auth BL33],
VD [auth A16S],
VE [auth A23S],
VF [auth A23S],
VG [auth A23S],
VH [auth AL15],
VI [auth B16S],
VJ [auth B16S],
VK [auth B23S],
VL [auth B23S],
VM [auth B23S],
VN [auth B23S],
VO [auth B23S],
VP [auth BL16],
VQ [auth BL33],
WD [auth A16S],
WE [auth A23S],
WF [auth A23S],
WG [auth A23S],
WH [auth AL15],
WI [auth B16S],
WJ [auth B16S],
WK [auth B23S],
WL [auth B23S],
WM [auth B23S],
WN [auth B23S],
WO [auth B23S],
WP [auth BL16],
WQ [auth BL34],
XD [auth A16S],
XE [auth A23S],
XF [auth A23S],
XG [auth A23S],
XH [auth AL17],
XI [auth B16S],
XJ [auth B16S],
XK [auth B23S],
XL [auth B23S],
XM [auth B23S],
XN [auth B23S],
XO [auth B23S],
XP [auth BL18],
XQ [auth BL34],
YD [auth A16S],
YE [auth A23S],
YF [auth A23S],
YG [auth A23S],
YH [auth AL17],
YI [auth B16S],
YJ [auth B16S],
YK [auth B23S],
YL [auth B23S],
YM [auth B23S],
YN [auth B23S],
YO [auth B23S],
YP [auth BL18],
YQ [auth BL35],
ZD [auth A16S],
ZE [auth A23S],
ZF [auth A23S],
ZG [auth A23S],
ZH [auth AL20],
ZI [auth B16S],
ZJ [auth B23S],
ZK [auth B23S],
ZL [auth B23S],
ZM [auth B23S],
ZN [auth B23S],
ZO [auth B23S],
ZP [auth BL18],
ZQ [auth BL36]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.271 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.45α = 90
b = 442.87β = 90
c = 613γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM118156

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-01
    Changes: Data collection, Database references
  • Version 2.0: 2019-07-03
    Changes: Data collection, Non-polymer description, Structure summary
  • Version 2.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description